Locus 6239

Sequence ID 3R_DroMel_CAF1
Location 16,291,931 – 16,292,091
Length 160
Max. P 0.758144
window10179 window10180 window10181

overview

Window 9

Location 16,291,931 – 16,292,051
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -41.62
Consensus MFE -41.62
Energy contribution -41.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 1.00
SVM decision value 0.14
SVM RNA-class probability 0.601552
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16291931 120 + 27905053
GUAACGCAGCCCGCCAUCAGGAGAGGUGGUUUUAAUUUGGAGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGA
.((((...(((.((((((......))))))........((((((((((.....((((((((........))))))))........)))))))))).)))...)))).............. ( -41.62)
>DroSec_CAF1 12591 120 + 1
GUAACGCAGCCCGCCAUCAGGAGAGGUGGUUUUAAUUUGGAGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGA
.((((...(((.((((((......))))))........((((((((((.....((((((((........))))))))........)))))))))).)))...)))).............. ( -41.62)
>DroSim_CAF1 4706 120 + 1
GUAACGCAGCCCGCCAUCAGGAGAGGUGGUUUUAAUUUGGAGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGA
.((((...(((.((((((......))))))........((((((((((.....((((((((........))))))))........)))))))))).)))...)))).............. ( -41.62)
>consensus
GUAACGCAGCCCGCCAUCAGGAGAGGUGGUUUUAAUUUGGAGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGA
.((((...(((.((((((......))))))........((((((((((.....((((((((........))))))))........)))))))))).)))...)))).............. (-41.62 = -41.62 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,291,931 – 16,292,051
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -38.20
Consensus MFE -38.20
Energy contribution -38.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 1.00
SVM decision value -0.03
SVM RNA-class probability 0.518764
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16291931 120 - 27905053
UCAAAACGGGUAGCUAACUGGGCCAAGAGCCCCUCAAUGAGGGCCCAUCUUCAAGAUGCAAAACGGGAUGAAGAGGGGCUCCAAAUUAAAACCACCUCUCCUGAUGGCGGGCUGCGUUAC
.........(((((.....((((.....)))).....((.((((((.((((((...((.....))...)))))).))))))))........((.((((....)).)).)))))))..... ( -38.20)
>DroSec_CAF1 12591 120 - 1
UCAAAACGGGUAGCUAACUGGGCCAAGAGCCCCUCAAUGAGGGCCCAUCUUCAAGAUGCAAAACGGGAUGAAGAGGGGCUCCAAAUUAAAACCACCUCUCCUGAUGGCGGGCUGCGUUAC
.........(((((.....((((.....)))).....((.((((((.((((((...((.....))...)))))).))))))))........((.((((....)).)).)))))))..... ( -38.20)
>DroSim_CAF1 4706 120 - 1
UCAAAACGGGUAGCUAACUGGGCCAAGAGCCCCUCAAUGAGGGCCCAUCUUCAAGAUGCAAAACGGGAUGAAGAGGGGCUCCAAAUUAAAACCACCUCUCCUGAUGGCGGGCUGCGUUAC
.........(((((.....((((.....)))).....((.((((((.((((((...((.....))...)))))).))))))))........((.((((....)).)).)))))))..... ( -38.20)
>consensus
UCAAAACGGGUAGCUAACUGGGCCAAGAGCCCCUCAAUGAGGGCCCAUCUUCAAGAUGCAAAACGGGAUGAAGAGGGGCUCCAAAUUAAAACCACCUCUCCUGAUGGCGGGCUGCGUUAC
.........(((((.....((((.....)))).....((.((((((.((((((...((.....))...)))))).))))))))........((.((((....)).)).)))))))..... (-38.20 = -38.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,291,971 – 16,292,091
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -38.13
Consensus MFE -38.02
Energy contribution -37.80
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 1.00
SVM decision value 0.49
SVM RNA-class probability 0.758144
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16291971 120 + 27905053
AGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGAGUGCAUAGCAAAUGAAGUUGGCAAUAAUAACCGGCAAUAC
.(((...((((((...(((.((((.(((.(((((((((((((...))))).....((((.......))))))))))))))))))).)))..))))))..))).................. ( -38.00)
>DroSec_CAF1 12631 120 + 1
AGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGAGUGCAUGGCAAAUGAAGUUGGCAAUAAUAACCGGCAAUUC
.(((...((((((...((..((((.(((.(((((((((((((...))))).....((((.......)))))))))))))))))))..))..))))))..))).................. ( -38.20)
>DroSim_CAF1 4746 120 + 1
AGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGAGUGCAUGGCAAAUGAAGUUGGCAAUAAUAACAGGCAAUUC
.(((...((((((...((..((((.(((.(((((((((((((...))))).....((((.......)))))))))))))))))))..))..))))))..))).................. ( -38.20)
>consensus
AGCCCCUCUUCAUCCCGUUUUGCAUCUUGAAGAUGGGCCCUCAUUGAGGGGCUCUUGGCCCAGUUAGCUACCCGUUUUGAGUGCAUGGCAAAUGAAGUUGGCAAUAAUAACCGGCAAUUC
.(((...((((((...(((.((((.(((.(((((((((((((...))))).....((((.......))))))))))))))))))).)))..))))))..))).................. (-38.02 = -37.80 +  -0.22)

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 12:16:29 2006