Locus 124

Sequence ID 3R_DroMel_CAF1
Location 681,743 – 681,871
Length 128
Max. P 0.902221
window204 window205

overview

Window 4

Location 681,743 – 681,839
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.20
Mean single sequence MFE -29.38
Consensus MFE -21.10
Energy contribution -21.06
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -2.30
Structure conservation index 0.72
SVM decision value 1.02
SVM RNA-class probability 0.902221
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 681743 96 + 27905053
AAAUAAACACACUC-----G------------AACACACUGUGUUGACACGUGUCAAAACUUCCGUUUGAAAUGGCUCGGAAAUGCUUCCGAGGCA-------CUCCGUGCUGGCCCUCU
.......(((((((-----(------------(((.....((.(((((....))))).))....))))))..((.(((((((....))))))).))-------....))).))....... ( -27.10)
>DroSec_CAF1 101142 96 + 1
AAACAAACACACUC-----G------------CACACACUGUGUUGACACGUGUCAAAACUUCCGUUUGAAAUGGCUCGGAAAUGCUUCCGAGGCA-------CUCCGUGCUGGCCCUCU
...(((((......-----(------------(((.....))))((((....))))........)))))....(((((((((....))))))((((-------(...))))).))).... ( -26.80)
>DroSim_CAF1 101400 96 + 1
AAACAAACACACUC-----G------------CACACACUGUGUUGACACGUGUCAAAACUUCCGUUUGAAAUGGCUCGGAAAUGCUUCCGAGGCA-------CUCCGUGCUGGCCCUCU
...(((((......-----(------------(((.....))))((((....))))........)))))....(((((((((....))))))((((-------(...))))).))).... ( -26.80)
>DroEre_CAF1 98457 112 + 1
AAACAAACACACACUCUCCACACUCCAGCACUCUAGCACUGUGUUGACACGUGUCAAAACUUCCGUUUGAAAUGGCUCGGAAAUGCUUCCGAGGCA-------CUCCGUGCUGGC-CUCU
........................(((((((((.(((...((.(((((....))))).))....))).))..((.(((((((....))))))).))-------....))))))).-.... ( -32.60)
>DroYak_CAF1 111072 109 + 1
AAACAAACAAACAC-----ACAAU------CUCUAGCACUGUGUUGACACGUGUCAAAACUUCCGUUUGAAAUGGCUCGGAAAUGCUUCCGAGGCACUUGGCACUUCGUGCUGGCCCUCU
..............-----.....------..(((((((.(((....)))((((((((((....))))....((.(((((((....))))))).))..))))))...)))))))...... ( -33.60)
>consensus
AAACAAACACACUC_____G____________CACACACUGUGUUGACACGUGUCAAAACUUCCGUUUGAAAUGGCUCGGAAAUGCUUCCGAGGCA_______CUCCGUGCUGGCCCUCU
.......(((((.......................((((.(((....)))))))..................((.(((((((....))))))).))...........))).))....... (-21.10 = -21.06 +  -0.04) 

alignment

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secondary structure

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dotplot

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Window 5

Location 681,766 – 681,871
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.35
Mean single sequence MFE -36.80
Consensus MFE -27.48
Energy contribution -27.68
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.75
SVM decision value 0.48
SVM RNA-class probability 0.751362
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 681766 105 - 27905053
UUACCCCAAUUUCG-GUUUCGAU-------GGCUUUUUUGAGAGGGCCAGCACGGAG-------UGCCUCGGAAGCAUUUCCGAGCCAUUUCAAACGGAAGUUUUGACACGUGUCAACAC
.......((((((.-((((.(.(-------(((((((....)))))))).)..((((-------((.(((((((....))))))).)))))))))).))))))(((((....)))))... ( -36.20)
>DroSec_CAF1 101165 105 - 1
UUACCCCAAUUUCG-GUUUCGAU-------GGCUUUUUUGAGAGGGCCAGCACGGAG-------UGCCUCGGAAGCAUUUCCGAGCCAUUUCAAACGGAAGUUUUGACACGUGUCAACAC
.......((((((.-((((.(.(-------(((((((....)))))))).)..((((-------((.(((((((....))))))).)))))))))).))))))(((((....)))))... ( -36.20)
>DroSim_CAF1 101423 105 - 1
UUACCCCAAUUUCG-GUUUCGAU-------GGCUUUUUUGAGAGGGCCAGCACGGAG-------UGCCUCGGAAGCAUUUCCGAGCCAUUUCAAACGGAAGUUUUGACACGUGUCAACAC
.......((((((.-((((.(.(-------(((((((....)))))))).)..((((-------((.(((((((....))))))).)))))))))).))))))(((((....)))))... ( -36.20)
>DroEre_CAF1 98497 105 - 1
UUACCCCAAUUUCGGGUUUCGAU-------GGCUUUUUUGAGAG-GCCAGCACGGAG-------UGCCUCGGAAGCAUUUCCGAGCCAUUUCAAACGGAAGUUUUGACACGUGUCAACAC
....(((......)))(((((.(-------((((((.....)))-))))....((((-------((.(((((((....))))))).))))))...)))))((.(((((....))))).)) ( -36.30)
>DroYak_CAF1 111101 120 - 1
UUACCCCAAUUUCGGGCUUCGAUGGCUGAUGGCUUUUUUGAGAGGGCCAGCACGAAGUGCCAAGUGCCUCGGAAGCAUUUCCGAGCCAUUUCAAACGGAAGUUUUGACACGUGUCAACAC
.......((((((((((((((...(((...(((((((....)))))))))).)))))).))(((((.(((((((....))))))).)))))......))))))(((((....)))))... ( -39.10)
>consensus
UUACCCCAAUUUCG_GUUUCGAU_______GGCUUUUUUGAGAGGGCCAGCACGGAG_______UGCCUCGGAAGCAUUUCCGAGCCAUUUCAAACGGAAGUUUUGACACGUGUCAACAC
..............................(((((((....))))))).(((((..........((.(((((((....))))))).))..((((((....).)))))..)))))...... (-27.48 = -27.68 +   0.20) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:51 2006