Locus 6259

Sequence ID 2R_DroMel_CAF1
Location 19,649,291 – 19,649,429
Length 138
Max. P 0.937573
window10013 window10014 window10015

overview

Window 3

Location 19,649,291 – 19,649,395
Length 104
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 87.28
Mean single sequence MFE -35.97
Consensus MFE -24.91
Energy contribution -25.69
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.72
Structure conservation index 0.69
SVM decision value 0.52
SVM RNA-class probability 0.766763
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19649291 104 + 20766785
UCCUGACUACGUGCCGCACCAAAGCCCUUCCACGAU------GAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGCA-------CUCCCGAGUCGCCCAAGUGUUUAAAACAC
...(((.(((((((.((......))(((((.(((((------(....))))))))))).))))((.((((.(((.......-------.))).)))).))....))).)))...... ( -29.80)
>DroEre_CAF1 6142 104 + 1
UCCUGACUACGUGCCGCACAAAAGCCCUUCCACGAU------GAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGUG-------CUCCGGAGUCCCCCAAGUGUUUAAAACAC
.........(((((.((......))(((((.(((((------(....))))))))))).))))).((((..((((((((..-------...))))))))....)))).......... ( -36.70)
>DroYak_CAF1 6289 117 + 1
UCCUGACUACGUGCCACACAAAGCCCCUUCCACGAUGAUGAUGAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGUUCCACGGUCUCCGGAGUCGCCCAAGUGUUUAAAACAC
..........((...((((...((.(((((.((((((..........))))))))))).))..((.((((((((..(((.....)))..)))))))).))....)))).....)).. ( -41.40)
>consensus
UCCUGACUACGUGCCGCACAAAAGCCCUUCCACGAU______GAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGUA_______CUCCGGAGUCGCCCAAGUGUUUAAAACAC
..........((...((((....(((((((.(((((............)))))))))).))..((.((((((((...............)))))))).))....)))).....)).. (-24.91 = -25.69 +   0.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,649,291 – 19,649,395
Length 104
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 87.28
Mean single sequence MFE -42.27
Consensus MFE -34.24
Energy contribution -34.69
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 0.81
SVM decision value 0.12
SVM RNA-class probability 0.594445
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19649291 104 - 20766785
GUGUUUUAAACACUUGGGCGACUCGGGAG-------UGCGGAGUCCGGAGUGGCGUGCUCCUUCACAACGUAAUC------AUCGUGGAAGGGCUUUGGUGCGGCACGUAGUCAGGA
............(((((((.((((.(((.-------(....).))).)))).))((((((((((...(((.....------..))).)))))((......)))))))....))))). ( -37.10)
>DroEre_CAF1 6142 104 - 1
GUGUUUUAAACACUUGGGGGACUCCGGAG-------CACGGAGUCCGGAGUGGCGUGCUCCUUCACAACGUAAUC------AUCGUGGAAGGGCUUUUGUGCGGCACGUAGUCAGGA
..........(((((...((((((((...-------..)))))))).)))))((((((((((((...(((.....------..))).)))))((......)))))))))........ ( -42.40)
>DroYak_CAF1 6289 117 - 1
GUGUUUUAAACACUUGGGCGACUCCGGAGACCGUGGAACGGAGUCCGGAGUGGCGUGCUCCUUCACAACGUAAUCAUCAUCAUCGUGGAAGGGGCUUUGUGUGGCACGUAGUCAGGA
(((((....((((....((.((((((((..(((.....)))..)))))))).))..((((((((...(((.............))).))))))))...))))))))).......... ( -47.32)
>consensus
GUGUUUUAAACACUUGGGCGACUCCGGAG_______AACGGAGUCCGGAGUGGCGUGCUCCUUCACAACGUAAUC______AUCGUGGAAGGGCUUUUGUGCGGCACGUAGUCAGGA
..........(((((.((..((((((............)))))))).)))))((((((((((((...(((.............))).)))))((......)))))))))........ (-34.24 = -34.69 +   0.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,649,327 – 19,649,429
Length 102
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 78.27
Mean single sequence MFE -28.70
Consensus MFE -19.73
Energy contribution -20.73
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.69
SVM decision value 1.26
SVM RNA-class probability 0.937573
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19649327 102 + 20766785
--GAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGCA-------CUCCCGAGUCGCCCAAGUGUUUAAAACACCCUUCAGCCUUCAGCCCUCAGACUUCAGACC-CCC
--......((((((((((.....((.((((.(((.......-------.))).)))).))....((((.....)))))))))).....))))................-... ( -21.60)
>DroEre_CAF1 6178 90 + 1
--GAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGUG-------CUCCGGAGUCCCCCAAGUGUUUAAAACACCCUGCAGCC-----CU--------UCAGACCUCCC
--......(((.((((((.((..((......((((((((..-------...)))))))).....((((.....))))...)).)))-----))--------))))))..... ( -29.30)
>DroYak_CAF1 6329 93 + 1
AUGAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGUUCCACGGUCUCCGGAGUCGCCCAAGUGUUUAAAACACCCUUCAGCC------------------GACC-CCC
........((((((((((.....((.((((((((..(((.....)))..)))))))).))....((((.....))))))))))..)------------------))).-... ( -35.20)
>consensus
__GAUUACGUUGUGAAGGAGCACGCCACUCCGGACUCCGUA_______CUCCGGAGUCGCCCAAGUGUUUAAAACACCCUUCAGCC_____C_________UCAGACC_CCC
............((((((.....((.((((((((...............)))))))).))....((((.....))))))))))............................. (-19.73 = -20.73 +   1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:49 2006