Locus 10217

Sequence ID 3R_DroMel_CAF1
Location 27,403,173 – 27,403,322
Length 149
Max. P 0.972291
window16271 window16272 window16273 window16274 window16275

overview

Window 1

Location 27,403,173 – 27,403,263
Length 90
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 80.44
Mean single sequence MFE -38.23
Consensus MFE -22.92
Energy contribution -22.95
Covariance contribution 0.03
Combinations/Pair 1.17
Mean z-score -1.71
Structure conservation index 0.60
SVM decision value 0.12
SVM RNA-class probability 0.591241
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27403173 90 - 27905053
GACCGAUGGGCAACAUGGGGCCCAUGGGA---GGUGGCCCGAUGGGCGGC------CCUAUGGGCGUAGGUCCCAAGCCGAUGACAAUGGGCGGCGGGA
..((.(((.....))).))(((((((((.---.((.((((...)))).))------))))))))).....((((..(((.((....)).)))...)))) ( -44.50)
>DroPse_CAF1 5727 93 - 1
GACCGAUGGGAAACAUGGGACCCAUGGGCGGCGGCGGGCCAAUGGGUGGA------CCGAUGGGAGUGGGACCCAAGCCGAUGACAAUGAGCGGUGGCA
..((.(((.....))).))...(((.((((((.....)))..(((((...------((.((....)).))))))).))).))).......((....)). ( -30.20)
>DroEre_CAF1 5561 90 - 1
GACCGAUGGGCAACAUGGGGCCCAUGGGU---GGUGGCCCGAUGGGCGGC------CCCAUGGGUGUAGGUCCCAAGCCGAUGACAAUGGGCGGCGGAA
..(((.((((..((...(.(((((((((.---.((.((((...)))).))------))))))))).)..)))))).(((.((....)).)))..))).. ( -44.30)
>DroWil_CAF1 5210 93 - 1
GUCCUAUGGGGAAUAUGGGCCCAAUGAGC------GGUCCAAUGGGUGGCGUAGGGCCAAUGGGCGUAGGGCCCAAGCCGAUGACAAUGAGUGGCGGUA
.(((.....)))...(((((((.(((...------(((((.(((.....))).)))))......))).))))))).((((.(.((.....)).))))). ( -34.60)
>DroAna_CAF1 5154 93 - 1
GCCCGAUGGGAAACAUGGGGCCAAUGGGUCCGGGUGGACCUAUGGGAGGG------CCCAUGGGCGUGGGGCCCAAGCCGAUGACAAUGGGUGGCGGCA
((((.(((.....))).))))...(((((((.(...(.((((((((....------))))))))).).))))))).((((.(.((.....)).))))). ( -45.60)
>DroPer_CAF1 5184 93 - 1
GACCGAUGGGAAACAUGGGACCCAUGGGCGGCGGCGGGCCAAUGGGUGGA------CCGAUGGGAGUGGGACCCAAGCCGAUGACAAUGAGCGGUGGCA
..((.(((.....))).))...(((.((((((.....)))..(((((...------((.((....)).))))))).))).))).......((....)). ( -30.20)
>consensus
GACCGAUGGGAAACAUGGGGCCCAUGGGC___GGUGGCCCAAUGGGUGGC______CCCAUGGGCGUAGGACCCAAGCCGAUGACAAUGAGCGGCGGCA
..((.(((.....))).))((((((.((..........)).)))))).........((..((((.......)))).((((...........)))))).. (-22.92 = -22.95 +   0.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 27,403,207 – 27,403,297
Length 90
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 88.79
Mean single sequence MFE -38.98
Consensus MFE -29.16
Energy contribution -29.77
Covariance contribution 0.61
Combinations/Pair 1.04
Mean z-score -4.51
Structure conservation index 0.75
SVM decision value 1.69
SVM RNA-class probability 0.972291
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27403207 90 + 27905053
GCCCAUAGGGCCGCCCAUCGGGCCACC---UCCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGACCUCCUCCACCACCGCC
((.(((.(((..((((((.(((.....---.)))))))))))))))...(((((.(((((....))))).)))))...............)). ( -37.10)
>DroSec_CAF1 5332 90 + 1
GCCCAUAGGGCCACCCAUCGGCCCACC---UCCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGUCCCAUGGGACCUCCUCCACCACCGCC
((.....(((((.......)))))...---((((((((((((..((..(((....))).))..))).)))))))))..............)). ( -36.90)
>DroSim_CAF1 4949 90 + 1
GCCCAUAGGGCCGCCCAUCGGCCCACC---UCCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGACCUCCUCCACCACCGCC
((.....((((((.....))))))...---((((((((((((..((..(((....))).))..))).)))))))))..............)). ( -38.60)
>DroEre_CAF1 5595 87 + 1
ACCCAUGGGGCCGCCCAUCGGGCCACC---ACCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCCGGACCCAUGGGUCCUCCUCCA---CCGCC
...(((((((((((((...))))...(---(....)))))))))))..((((((.(((((....))))).)))))).........---..... ( -41.60)
>DroYak_CAF1 4898 90 + 1
ACCCAUUGGGCCGCCCAUCGGGCCACC---ACCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGUCCUCCUCCACCACCGCC
......((((..((((((.(((.....---.)))))))))))))....((((((.(((((....))))).))))))................. ( -38.00)
>DroAna_CAF1 5188 93 + 1
GCCCAUGGGCCCUCCCAUAGGUCCACCCGGACCCAUUGGCCCCAUGUUUCCCAUCGGGCCGCCAGGUCCCAUGGGUCCUACUCCGCCCCCACC
(((((((((.(((..(...(((((....)))))....(((((.(((.....))).))))))..))).)))))))))................. ( -41.70)
>consensus
GCCCAUAGGGCCGCCCAUCGGGCCACC___ACCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGACCUCCUCCACCACCGCC
...(((.(((..((((((.((..........)).))))))))))))...(((((.(((((....))))).))))).................. (-29.16 = -29.77 +   0.61)

alignment

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secondary structure

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dotplot

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Window 3

Location 27,403,207 – 27,403,297
Length 90
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 88.79
Mean single sequence MFE -45.87
Consensus MFE -35.04
Energy contribution -35.35
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -3.04
Structure conservation index 0.76
SVM decision value 0.42
SVM RNA-class probability 0.728054
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27403207 90 - 27905053
GGCGGUGGUGGAGGAGGUCCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGA---GGUGGCCCGAUGGGCGGCCCUAUGGGC
(.(.((((.........((((((((((((((((.(.((....))).)).))))))))))))))---(((.((((...)))).))))))).).) ( -47.70)
>DroSec_CAF1 5332 90 - 1
GGCGGUGGUGGAGGAGGUCCCAUGGGACCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGA---GGUGGGCCGAUGGGUGGCCCUAUGGGC
(.(.(((..........(((((((((.(((.(((..((....))...))).))))))))))))---...((((((.....))))))))).).) ( -42.10)
>DroSim_CAF1 4949 90 - 1
GGCGGUGGUGGAGGAGGUCCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGA---GGUGGGCCGAUGGGCGGCCCUAUGGGC
(.(.(((..........((((((((((((((((.(.((....))).)).))))))))))))))---...((((((.....))))))))).).) ( -45.60)
>DroEre_CAF1 5595 87 - 1
GGCGG---UGGAGGAGGACCCAUGGGUCCGGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGU---GGUGGCCCGAUGGGCGGCCCCAUGGGU
..(.(---((......(.(((((.(((((....))))).))))))..))).).(((((((((.---.((.((((...)))).))))))))))) ( -46.90)
>DroYak_CAF1 4898 90 - 1
GGCGGUGGUGGAGGAGGACCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGU---GGUGGCCCGAUGGGCGGCCCAAUGGGU
..((.((..........((((((((((((((((.(.((....))).)).))))))))))))))---(((.((((...)))).))))).))... ( -43.80)
>DroAna_CAF1 5188 93 - 1
GGUGGGGGCGGAGUAGGACCCAUGGGACCUGGCGGCCCGAUGGGAAACAUGGGGCCAAUGGGUCCGGGUGGACCUAUGGGAGGGCCCAUGGGC
.(((((..(......)..))))).(((((((..(((((.(((.....))).)))))..))))))).......((((((((....)))))))). ( -49.10)
>consensus
GGCGGUGGUGGAGGAGGACCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGA___GGUGGCCCGAUGGGCGGCCCUAUGGGC
.((...............(((((.(((((....))))).)))))...((((((((((((.((..........)).)))...))))))))).)) (-35.04 = -35.35 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 27,403,226 – 27,403,322
Length 96
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 83.22
Mean single sequence MFE -39.98
Consensus MFE -29.83
Energy contribution -29.88
Covariance contribution 0.06
Combinations/Pair 1.20
Mean z-score -3.28
Structure conservation index 0.75
SVM decision value 1.11
SVM RNA-class probability 0.916565
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27403226 96 + 27905053
GGGCCACC---UCCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGACCUCCUCCACCACCGCCGAACAUAUUUGGACCUGGGCC------GCCC
((((....---((((((((((((..((..(((....))).))..))).))))))))).........(((...(((((....)))))...)))...------)))) ( -38.90)
>DroSim_CAF1 4968 96 + 1
GGCCCACC---UCCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGACCUCCUCCACCACCGCCGAACAUAUUGGGACCUGGGCC------GCCC
((((((..---((((((((((........)))))(((((((....)))))..((((......))))........))......)))))..))))))------.... ( -40.20)
>DroEre_CAF1 5614 93 + 1
GGGCCACC---ACCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCCGGACCCAUGGGUCCUCCUCCA---CCGCCGAACAUAUUUGGACCUGGUCC------ACCC
((((((..---....((((((........)))))).((((((...(((((....)))))...((..---.....)).......))))))))))))------.... ( -36.40)
>DroYak_CAF1 4917 96 + 1
GGGCCACC---ACCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGUCCUCCUCCACCACCGCCGAACAUAUUUGGACCUGGUCC------GCCC
((((....---((((((((((((..((..(((....))).))..))).)))))))))........((((...(((((....)))))...))))..------)))) ( -38.80)
>DroAna_CAF1 5207 105 + 1
GGUCCACCCGGACCCAUUGGCCCCAUGUUUCCCAUCGGGCCGCCAGGUCCCAUGGGUCCUACUCCGCCCCCACCAAACAUAUUUGGCCCUGGUCCGGGCCCACCC
(((...((((((((....((((..(((((((((((.(((((....))))).)))))..................))))))....))))..))))))))...))). ( -44.16)
>DroPer_CAF1 5237 93 + 1
GGCCCGCCGCCGCCCAUGGGUCCCAUGUUUCCCAUCGGUCCGCCAGGACCCAUGGGUCCUC------CGCCGCCAAACAUAUUGGGUCCGGGGCC------ACCC
(((((((.(..((((((((((((.(((.....))).((....)).))))))))))))...)------.))..((((.....)))).....)))))------.... ( -41.40)
>consensus
GGGCCACC___ACCCAUGGGCCCCAUGUUGCCCAUCGGUCCACCGGGACCCAUGGGUCCUCCUCCACCACCGCCGAACAUAUUUGGACCUGGGCC______ACCC
(((((......((((((((((........))))...(((((....))))).))))))...............(((((....)))))....))))).......... (-29.83 = -29.88 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 27,403,226 – 27,403,322
Length 96
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 83.22
Mean single sequence MFE -48.52
Consensus MFE -30.50
Energy contribution -31.42
Covariance contribution 0.92
Combinations/Pair 1.21
Mean z-score -2.75
Structure conservation index 0.63
SVM decision value 0.39
SVM RNA-class probability 0.717014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27403226 96 - 27905053
GGGC------GGCCCAGGUCCAAAUAUGUUCGGCGGUGGUGGAGGAGGUCCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGA---GGUGGCCC
((((------.(((....((((....((.....))....)))).....((((((((((((((((.(.((....))).)).))))))))))))))---))).)))) ( -49.70)
>DroSim_CAF1 4968 96 - 1
GGGC------GGCCCAGGUCCCAAUAUGUUCGGCGGUGGUGGAGGAGGUCCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGA---GGUGGGCC
....------((((((..(((((...(.(((.((....)).))).)(((((((((.(((((((....)))..))))..)))))))))..)))))---..)))))) ( -49.90)
>DroEre_CAF1 5614 93 - 1
GGGU------GGACCAGGUCCAAAUAUGUUCGGCGG---UGGAGGAGGACCCAUGGGUCCGGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGU---GGUGGCCC
((((------.(.((...((((....((.....)).---)))).....((((((((((((((.....))....(....)...))))))))))))---))).)))) ( -41.20)
>DroYak_CAF1 4917 96 - 1
GGGC------GGACCAGGUCCAAAUAUGUUCGGCGGUGGUGGAGGAGGACCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGU---GGUGGCCC
((((------.(.((...((((....((.....))....)))).....((((((((((((((((.(.((....))).)).))))))))))))))---))).)))) ( -46.50)
>DroAna_CAF1 5207 105 - 1
GGGUGGGCCCGGACCAGGGCCAAAUAUGUUUGGUGGGGGCGGAGUAGGACCCAUGGGACCUGGCGGCCCGAUGGGAAACAUGGGGCCAAUGGGUCCGGGUGGACC
.(((..(((((((((...((((.....((((.(((((..(......)..))))).)))).))))(((((.(((.....))).)))))....)))))))))..))) ( -58.10)
>DroPer_CAF1 5237 93 - 1
GGGU------GGCCCCGGACCCAAUAUGUUUGGCGGCG------GAGGACCCAUGGGUCCUGGCGGACCGAUGGGAAACAUGGGACCCAUGGGCGGCGGCGGGCC
....------((((((((((.......)))))((.((.------(....((((((((((((((....))....(....)..))))))))))))).)).))))))) ( -45.70)
>consensus
GGGC______GGACCAGGUCCAAAUAUGUUCGGCGGUGGUGGAGGAGGACCCAUGGGUCCCGGUGGACCGAUGGGCAACAUGGGGCCCAUGGGU___GGUGGCCC
..........((.(((...((.......(((.((....)).)))....(((((((((((((((....))....(....)..)))))))))))))...))))).)) (-30.50 = -31.42 +   0.92)

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 13:51:43 2006