Locus 1247

Sequence ID 3R_DroMel_CAF1
Location 3,747,576 – 3,747,800
Length 224
Max. P 0.873377
window2030 window2031 window2032

overview

Window 0

Location 3,747,576 – 3,747,672
Length 96
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 78.22
Mean single sequence MFE -19.86
Consensus MFE -9.90
Energy contribution -10.90
Covariance contribution 1.00
Combinations/Pair 1.32
Mean z-score -1.89
Structure conservation index 0.50
SVM decision value 0.14
SVM RNA-class probability 0.601907
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3747576 96 - 27905053
UAA-GGCAAAAGAUAGUCUUUGGUUUUUAGGUACUAGCAAUAAUUGCAUAGGACUUGAAAAUACAUCCUAAGACUAUAUAUUAGAC-GAACUAACUUG
(((-(.......((((((((.(((((((((((.((((((.....))).))).))))))))).....)).))))))))...((((..-...)))))))) ( -21.90)
>DroSec_CAF1 1219 91 - 1
AAA-GGCAAAAGAUAGUCU-UGGUUUUUAGGUACUAGCAAUAAUUGCAGAGGACUUGAAAAUACAUCCUAAGACUAUUUAUUCGAC-GAA----CUUG
...-......(((((((((-((((((((((((.((.(((.....)))..)).)))))))))......)))))))))))).......-...----.... ( -21.40)
>DroSim_CAF1 1215 91 - 1
AAA-CGCAAAAGAUAGUCU-UGGUUUUUAGGUACUAACAAUAAUUGCAGAGGACUUGAAAAUACAUCCUAAGACUAUUUAUUCGAC-GAA----CUUU
...-((.((.(((((((((-((((((((((((.((..((.....))...)).)))))))))......)))))))))))).))))..-...----.... ( -19.80)
>DroEre_CAF1 1212 92 - 1
AAAAGGCAAAA-AUAGUCGUUGGUUUUCAAGUUU-CUGAAUAAUUGCAGAGGCUUUGAAAAUAUCUCCCAAGACUGU-UAUUCACA-GAACUAACU--
..........(-((((((.(((((((((((((((-(((........))))))).)))))))......))))))))))-).......-.........-- ( -22.50)
>DroYak_CAF1 1173 96 - 1
AAGAGGCAAAAUAUAGUCGUCGGUUUUAAAGUUU-UCCCAUAAUUGCAGAGGAUUGGAAAAUAUCUCCUAAGACUAU-AAUUCUAACUAACUAACUUG
...........(((((((...((.......((((-(((.((..((...))..)).)))))))....))...))))))-)................... ( -13.70)
>consensus
AAA_GGCAAAAGAUAGUCUUUGGUUUUUAGGUACUAGCAAUAAUUGCAGAGGACUUGAAAAUACAUCCUAAGACUAU_UAUUCGAC_GAACUAACUUG
............((((((((.(((((((((((.(((............))).))))))))).....)).))))))))..................... ( -9.90 = -10.90 +   1.00)

alignment

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secondary structure

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Window 1

Location 3,747,672 – 3,747,774
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 89.22
Mean single sequence MFE -36.83
Consensus MFE -31.77
Energy contribution -31.08
Covariance contribution -0.69
Combinations/Pair 1.31
Mean z-score -1.99
Structure conservation index 0.86
SVM decision value 0.88
SVM RNA-class probability 0.873377
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3747672 102 + 27905053
CUCCAUGUGAUGAGUCAGAACGGAUAUCUGAGAAGCGUGCUCAUACUUGGCAGUCGCUGGGCACGAGUUACUGUGCGGUGGCUGUCCAAGAGCAGGCCAUGA
...((((.......(((((.......)))))...((.(((((....(((((((((((((.(((........))).))))))))).))))))))).)))))). ( -39.90)
>DroSec_CAF1 1310 102 + 1
GUUCAUGUGAUGAGUCAGAACGGAUAUCUGAGAUGCGUGCUCAUACUUGGGAGUCGCUGGGCACGAGUUACUGUGCGGUGGCUGUCCAAGAGCAGGCCAUGA
..(((((.......(((((.......)))))...((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).))))))) ( -37.70)
>DroSim_CAF1 1306 102 + 1
GUUCAUGUGAUGAGUCAGAACGGAUAUCUGAGAUGCGUGCUCAUACUUGGAAGUCGCUGGGCACGAGUUACUGUGCGGUGGCUGUCCAAGAGCAGGCCAUGA
..(((((.......(((((.......)))))...((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).))))))) ( -38.20)
>DroEre_CAF1 1304 102 + 1
GUCCAUGUGAUGACUCAGAACGGAUAUCUGAGAAGCGUGCUCAUACUUGGGAGCCGCUGGGCACGAGUUACUGUGCGGCGGCUGUUCAAGAGCACGCCAAGA
.............((((((.......))))))..((((((((....(((((((((((((.(((........))).)))))))).)))))))))))))..... ( -42.80)
>DroYak_CAF1 1269 102 + 1
GUCCAUGUGAUGAGUCAGAACGGAUAUCUGAGAAGCGUGUUCAUACUUGGGAGUCGCUGGGCACGAGUUACUGUGCGGCGGCUGUUCAAGAGCAGGCCAUGA
...((((.......(((((.......)))))...((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).)))))). ( -33.90)
>DroAna_CAF1 1195 100 + 1
GUAAUCAUGAUGAGUCAGAACGGAUAUCUGAGUAACUUGCUUAUAUUUGGG-GUCGUUGGGCACGAGUUACUGUGCGACGGUCAU-CAAGAGCAAGUCAAGA
....((.(((..(.(((((.......))))).)..(((((((....(((((-..(((((.(((........))).)))))..).)-))))))))))))).)) ( -28.50)
>consensus
GUCCAUGUGAUGAGUCAGAACGGAUAUCUGAGAAGCGUGCUCAUACUUGGGAGUCGCUGGGCACGAGUUACUGUGCGGCGGCUGUCCAAGAGCAGGCCAUGA
...((((.......(((((.......)))))...((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).)))))). (-31.77 = -31.08 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,747,706 – 3,747,800
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 86.17
Mean single sequence MFE -31.38
Consensus MFE -27.22
Energy contribution -26.08
Covariance contribution -1.13
Combinations/Pair 1.39
Mean z-score -1.65
Structure conservation index 0.87
SVM decision value 0.35
SVM RNA-class probability 0.701821
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3747706 94 + 27905053
GCGUGCUCAUACUUGGCAGUCGCUGGGCACGAGUUACUGUGCGGUGGCUGUCCAAGAGCAGGCCAUGAUUAAAACCUCGAAUACUGAAUAAGUG
((.(((((....(((((((((((((.(((........))).))))))))).))))))))).))..................((((.....)))) ( -33.70)
>DroSec_CAF1 1344 94 + 1
GCGUGCUCAUACUUGGGAGUCGCUGGGCACGAGUUACUGUGCGGUGGCUGUCCAAGAGCAGGCCAUGAUUAAAACCUCGAAUACUGAAUAAGUG
((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).))..................((((.....)))) ( -31.00)
>DroSim_CAF1 1340 94 + 1
GCGUGCUCAUACUUGGAAGUCGCUGGGCACGAGUUACUGUGCGGUGGCUGUCCAAGAGCAGGCCAUGAUUAAAACCUCGAAUACUGAUUAAGUG
((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).))..................((((.....)))) ( -31.50)
>DroEre_CAF1 1338 94 + 1
GCGUGCUCAUACUUGGGAGCCGCUGGGCACGAGUUACUGUGCGGCGGCUGUUCAAGAGCACGCCAAGAUUAAAACGUCGAGUACUGAACAGUUG
((((((((....(((((((((((((.(((........))).)))))))).))))))))))))).........(((.(((.....)))...))). ( -36.60)
>DroYak_CAF1 1303 94 + 1
GCGUGUUCAUACUUGGGAGUCGCUGGGCACGAGUUACUGUGCGGCGGCUGUUCAAGAGCAGGCCAUGAUUAAAGCUUCGAAUACUGAAUAAUUG
..((((((...((((((((((((((.(((........))).)))))))).)))))).(.((((..........))))))))))).......... ( -29.70)
>DroAna_CAF1 1229 91 + 1
ACUUGCUUAUAUUUGGG-GUCGUUGGGCACGAGUUACUGUGCGACGGUCAU-CAAGAGCAAGUCAAGAUUAAAGAUUCCAAGCCUGAAA-GGUU
((((((((....(((((-..(((((.(((........))).)))))..).)-))))))))))).................((((.....-)))) ( -25.80)
>consensus
GCGUGCUCAUACUUGGGAGUCGCUGGGCACGAGUUACUGUGCGGCGGCUGUCCAAGAGCAGGCCAUGAUUAAAACCUCGAAUACUGAAUAAGUG
((.(((((....(((((((((((((.(((........))).)))))))).)))))))))).))............................... (-27.22 = -26.08 +  -1.13)

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 10:04:33 2006