Locus 2074

Sequence ID 3R_DroMel_CAF1
Location 5,895,833 – 5,896,091
Length 258
Max. P 0.996131
window3385 window3386 window3387 window3388 window3389

overview

Window 5

Location 5,895,833 – 5,895,932
Length 99
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 73.72
Mean single sequence MFE -22.96
Consensus MFE -17.08
Energy contribution -17.19
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -1.84
Structure conservation index 0.74
SVM decision value 2.48
SVM RNA-class probability 0.994436
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5895833 99 + 27905053
ACAAACA---CCAUUUACACCACUCCACACCCCACAGCUAGCCACCCACAA--------AAGUCAUGUGGAAUGGGUGGCUUAAACUCCAACGUAGUGCAAUGAAAUUCU
.......---.((((..(((.((............(((((.(((.(((((.--------......)))))..))).)))))...........)).))).))))....... ( -19.00)
>DroEre_CAF1 20567 101 + 1
ACAAGCAGAAGCUCCUUU---------UUUCCCCCAGUUAGCCACCCACAAACACACAAAAGCCAUGUGGAGUGGGUGGCUAAAACUCCAAAGCAGUGCAAUGAAAUUCU
.....((...(((.((((---------..........((((((((((((...((((.........))))..))))))))))))......)))).)))....))....... ( -28.69)
>DroYak_CAF1 19692 92 + 1
AGAAACA---CCUUCUUU---------UUCCCCCCAGCUAGCCACCCACAAGU------GGGCCAUGUGGAGUGGGUGGCUUAAACUCCAACGCAGUGCAAUGAAAUUCU
((((...---........---------........(((((.(((((((((.(.------....).))))).)))).)))))...........((...)).......)))) ( -21.20)
>consensus
ACAAACA___CCUUCUUU_________UUCCCCCCAGCUAGCCACCCACAA________AAGCCAUGUGGAGUGGGUGGCUUAAACUCCAACGCAGUGCAAUGAAAUUCU
...................................(((((.(((((((((...............))))).)))).)))))............................. (-17.08 = -17.19 +   0.11)

alignment

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secondary structure

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Window 6

Location 5,895,833 – 5,895,932
Length 99
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 73.72
Mean single sequence MFE -31.98
Consensus MFE -23.34
Energy contribution -23.45
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.73
SVM decision value 2.66
SVM RNA-class probability 0.996131
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5895833 99 - 27905053
AGAAUUUCAUUGCACUACGUUGGAGUUUAAGCCACCCAUUCCACAUGACUU--------UUGUGGGUGGCUAGCUGUGGGGUGUGGAGUGGUGUAAAUGG---UGUUUGU
.((((.((((((((((((...........((((((((((............--------..)))))))))).(((....))).....))))))).)))))---.)))).. ( -32.04)
>DroEre_CAF1 20567 101 - 1
AGAAUUUCAUUGCACUGCUUUGGAGUUUUAGCCACCCACUCCACAUGGCUUUUGUGUGUUUGUGGGUGGCUAACUGGGGGAAA---------AAAGGAGCUUCUGCUUGU
.((((((((..((...))..))))))))(((((((((((..((((..(...)..))))...)))))))))))...........---------....((((....)))).. ( -37.30)
>DroYak_CAF1 19692 92 - 1
AGAAUUUCAUUGCACUGCGUUGGAGUUUAAGCCACCCACUCCACAUGGCCC------ACUUGUGGGUGGCUAGCUGGGGGGAA---------AAAGAAGG---UGUUUCU
.((((((((.(((...))).)))))))).((((((((((............------....))))))))))........((((---------(.......---..))))) ( -26.59)
>consensus
AGAAUUUCAUUGCACUGCGUUGGAGUUUAAGCCACCCACUCCACAUGGCUU________UUGUGGGUGGCUAGCUGGGGGGAA_________AAAGAAGG___UGUUUGU
.((((((((.((.....)).)))))))).((((((((((......................))))))))))....................................... (-23.34 = -23.45 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,895,870 – 5,895,972
Length 102
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 87.65
Mean single sequence MFE -30.73
Consensus MFE -26.96
Energy contribution -26.63
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -2.20
Structure conservation index 0.88
SVM decision value 0.94
SVM RNA-class probability 0.886257
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5895870 102 + 27905053
GCCACCCACAA--------AAGUCAUGUGGAAUGGGUGGCUUAAACUCCAACGUAGUGCAAUGAAAUUCUUCAUCUACAAUUCAAUGACAUUCCAUUCUGGGCUUUGGAC
.....(((...--------(((((..((((((((((.(.......).))...((((....(((((....)))))))))..........))))))))....)))))))).. ( -24.90)
>DroEre_CAF1 20598 110 + 1
GCCACCCACAAACACACAAAAGCCAUGUGGAGUGGGUGGCUAAAACUCCAAAGCAGUGCAAUGAAAUUCUUCAUCUGCAAUUCAAUGACAUUCCAUUCCGGGCCUUGGAC
(((((((((...((((.........))))..)))))))))......(((((.((..(((((((((....))))).)))).............((.....)))).))))). ( -37.40)
>DroYak_CAF1 19720 104 + 1
GCCACCCACAAGU------GGGCCAUGUGGAGUGGGUGGCUUAAACUCCAACGCAGUGCAAUGAAAUUCUUCAUCUACAAUUCAAUGACAUUCCAUUCCGGGCCUUGGGC
....((((.....------(((((..((((((((((.(.......).))......(((..(((((....))))).)))..........))))))))....))))))))). ( -29.90)
>consensus
GCCACCCACAA________AAGCCAUGUGGAGUGGGUGGCUUAAACUCCAACGCAGUGCAAUGAAAUUCUUCAUCUACAAUUCAAUGACAUUCCAUUCCGGGCCUUGGAC
(((((((((.............((....)).)))))))))......(((((.((((((((.((((...............)))).)).))))((.....)))).))))). (-26.96 = -26.63 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,895,870 – 5,895,972
Length 102
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 87.65
Mean single sequence MFE -37.78
Consensus MFE -31.70
Energy contribution -32.15
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -3.00
Structure conservation index 0.84
SVM decision value 1.45
SVM RNA-class probability 0.955106
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5895870 102 - 27905053
GUCCAAAGCCCAGAAUGGAAUGUCAUUGAAUUGUAGAUGAAGAAUUUCAUUGCACUACGUUGGAGUUUAAGCCACCCAUUCCACAUGACUU--------UUGUGGGUGGC
.(((((......(((((((((.(((((........)))))...)))))))).)......)))))......(((((((((............--------..))))))))) ( -29.84)
>DroEre_CAF1 20598 110 - 1
GUCCAAGGCCCGGAAUGGAAUGUCAUUGAAUUGCAGAUGAAGAAUUUCAUUGCACUGCUUUGGAGUUUUAGCCACCCACUCCACAUGGCUUUUGUGUGUUUGUGGGUGGC
.((((((((..(.((((((((.(((((........)))))...)))))))).)...))))))))......(((((((((..((((..(...)..))))...))))))))) ( -46.30)
>DroYak_CAF1 19720 104 - 1
GCCCAAGGCCCGGAAUGGAAUGUCAUUGAAUUGUAGAUGAAGAAUUUCAUUGCACUGCGUUGGAGUUUAAGCCACCCACUCCACAUGGCCC------ACUUGUGGGUGGC
((((((.((..(.((((((((.(((((........)))))...)))))))).)...)).)))).))....(((((((((............------....))))))))) ( -37.19)
>consensus
GUCCAAGGCCCGGAAUGGAAUGUCAUUGAAUUGUAGAUGAAGAAUUUCAUUGCACUGCGUUGGAGUUUAAGCCACCCACUCCACAUGGCUU________UUGUGGGUGGC
.(((((.((...(((((((((.(((((........)))))...)))))))).)...)).)))))......(((((((((......................))))))))) (-31.70 = -32.15 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,895,972 – 5,896,091
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.54
Mean single sequence MFE -58.83
Consensus MFE -53.37
Energy contribution -54.03
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.54
Structure conservation index 0.91
SVM decision value 1.15
SVM RNA-class probability 0.922603
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5895972 119 + 27905053
GGGGCGUGGCAAGUUGCAGGACGCUGCCAAUAAGCGUGCCC-CCAGUGGAGCAACAGAUGAUACAUUUAUGCAGCGCCCCCUCGUGGGCCUGCAUCAGGGGGCGUGGCUGCGCAUGCGCC
((.((((((((.((..(...(((((.......)))))((((-((((((...((.....))...)))).((((((.((((......))))))))))..)))))))..))))).))))).)) ( -58.70)
>DroEre_CAF1 20708 119 + 1
GGGGCGUGGCAAGUCGGAGAAGGCUGCCAAUAAGCGUGCCCCCCAGUGGAGCAACAGAUGAUACAU-UAUGCAGCGCCCCCUGGUGGGCCUGCAUCAGGGGGCGUGGCGGCGCAUGCGCC
..(((.(((((.(((......))))))))....((((((((.((......(((...((((...)))-).))).(((((((((((((......))))))))))))))).)).))))))))) ( -60.20)
>DroYak_CAF1 19824 119 + 1
GGGGCGUGGCAAGUCGGAGAAGGCUGCCAAUAAGCGUGCCCCCCAGUGGAGCAACAGAUGAUACAU-UAUGCAGCGCCCCCUGGUGGGCCUGCAUCAGGGGGCGUGGCUGCGCAUGCGCC
..(((.(((((.(((......))))))))....((((((.....((((...((.....))...)))-)..((((((((((((((((......)))))))))))...)))))))))))))) ( -57.60)
>consensus
GGGGCGUGGCAAGUCGGAGAAGGCUGCCAAUAAGCGUGCCCCCCAGUGGAGCAACAGAUGAUACAU_UAUGCAGCGCCCCCUGGUGGGCCUGCAUCAGGGGGCGUGGCUGCGCAUGCGCC
..(((((((((.(((......))))))).....((((((((......)).))..................((.(((((((((((((......))))))))))))).)).))))..))))) (-53.37 = -54.03 +   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 10:26:42 2006