Locus 2394

Sequence ID X_DroMel_CAF1
Location 6,404,626 – 6,404,774
Length 148
Max. P 0.801641
window3894 window3895 window3896

overview

Window 4

Location 6,404,626 – 6,404,734
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 94.14
Mean single sequence MFE -26.86
Consensus MFE -23.92
Energy contribution -23.55
Covariance contribution -0.37
Combinations/Pair 1.18
Mean z-score -1.49
Structure conservation index 0.89
SVM decision value 0.13
SVM RNA-class probability 0.600224
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6404626 108 - 22224390
GAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAUUCUUCUUUGACCUUGGUUUGAGGUGAUUUCUUCU
((((.(((((.((((((.......((..(((.....)))..))....)))))).....))))).))))(.(((.((.((((.(((....))).)))).))..))).). ( -26.60)
>DroSec_CAF1 30044 108 - 1
GAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAUUCUUCUUUGGGCUUAGUUUGAGGUGAUUUCUUCU
(((((..((((((((((((....((..((((.....))).......((((..(...)..))))...)..))((....))...))))))))...))))..))))).... ( -27.50)
>DroSim_CAF1 29175 108 - 1
GAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAUUCUUCUUUGAUCUUAGUUUGAGGCGAUUUCUUCU
((((((((...((((((.......((..(((.....)))..))....))))))..((..(((.......((((......))))......)))..)))))))))).... ( -25.12)
>DroYak_CAF1 33391 108 - 1
GAGGUUGCUUUUUAGGCUCCCAUUGUGAAACUUUUUGUGGAACCUUUGCCUGAUAUUUAGGCACCUUUGCAGGUUCUUCCUUGAGCUUAGUUUGAGGUGAUUUUUUCU
(((((((((.....)))..((((.............)))))))))).((((((...))))))(((((.((((((((......)))))).))..))))).......... ( -28.22)
>consensus
GAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAUUCUUCUUUGAGCUUAGUUUGAGGUGAUUUCUUCU
(((((((((((((((((((....((..((((.....))).......(((((((...)))))))...)..))((....))...))))))))...))))))))))).... (-23.92 = -23.55 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,404,660 – 6,404,774
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 93.86
Mean single sequence MFE -28.68
Consensus MFE -22.22
Energy contribution -23.47
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.77
SVM decision value -0.03
SVM RNA-class probability 0.517271
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6404660 114 + 22224390
AUCUGCAAGGGUGCCCAAGUAUCAGGCAAAGGUUUCACAAAAAGUGUCACAAUGGGAGCCUAAAAAGCAACCUCAAAGGGAGCCAAAGGUAACUCAAAAGGAAACCCCAUUGGA
...(((...(((((....)))))..))).......(((.....)))...(((((((.((((.....((..((.....))..))...)))).........(....)))))))).. ( -28.20)
>DroSec_CAF1 30078 114 + 1
AUCUGCAAGGGUGCCCAAGUAUCAGGCAAAGGUUUCACAAAAAGUGUCACAAUGGGAGCCUAAAAAGCAACCUCAAAGGGAGCCAAAGGUGACUCAAAAGGAAACCCCAUGGGA
...(((...(((((....)))))..)))..((((((.........(((((....((..(((....((....))....)))..))....))))).......))))))........ ( -28.39)
>DroSim_CAF1 29209 114 + 1
AUCUGCAAGGGUGCCCAAGUAUCAGGCAAAGGUUUCACAAAAAGUGUCACAAUGGGAGCCUAAAAAGCAACCUCAAAGGGAGCCGAAGGUGACUCAAAAGGAAACCCCAUGGGA
...(((...(((((....)))))..)))..((((((.........(((((..(.((..(((....((....))....)))..)).)..))))).......))))))........ ( -28.49)
>DroYak_CAF1 33425 114 + 1
ACCUGCAAAGGUGCCUAAAUAUCAGGCAAAGGUUCCACAAAAAGUUUCACAAUGGGAGCCUAAAAAGCAACCUCUACGGGAGCCAAAGGUGUCACAAAAAGAAACCCCAUGGGA
.((((...((((((((.......))))..(((((((.((.............)))))))))........))))...))))..(((..(((.((.......)).)))...))).. ( -29.62)
>consensus
AUCUGCAAGGGUGCCCAAGUAUCAGGCAAAGGUUUCACAAAAAGUGUCACAAUGGGAGCCUAAAAAGCAACCUCAAAGGGAGCCAAAGGUGACUCAAAAGGAAACCCCAUGGGA
...(((...(((((....)))))..)))..((((((.........(((((....((..(((....((....))....)))..))....))))).......))))))........ (-22.22 = -23.47 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,404,660 – 6,404,774
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 93.86
Mean single sequence MFE -31.68
Consensus MFE -27.00
Energy contribution -26.75
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.88
Structure conservation index 0.85
SVM decision value 0.62
SVM RNA-class probability 0.801641
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6404660 114 - 22224390
UCCAAUGGGGUUUCCUUUUGAGUUACCUUUGGCUCCCUUUGAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAU
((((((((((...(((...((((.(((((.((...))...))))).))))...))).)))))))).)).....((((..(......((((..(...)..))))...)..)))). ( -33.90)
>DroSec_CAF1 30078 114 - 1
UCCCAUGGGGUUUCCUUUUGAGUCACCUUUGGCUCCCUUUGAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAU
.....(((((...(((...((((.(((((.((...))...))))).))))...))).)))))(((..((((.....))).......((((..(...)..))))...)..))).. ( -30.60)
>DroSim_CAF1 29209 114 - 1
UCCCAUGGGGUUUCCUUUUGAGUCACCUUCGGCUCCCUUUGAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAU
.....(((((...(((...((((.(((((.((...))...))))).))))...))).)))))(((..((((.....))).......((((..(...)..))))...)..))).. ( -29.20)
>DroYak_CAF1 33425 114 - 1
UCCCAUGGGGUUUCUUUUUGUGACACCUUUGGCUCCCGUAGAGGUUGCUUUUUAGGCUCCCAUUGUGAAACUUUUUGUGGAACCUUUGCCUGAUAUUUAGGCACCUUUGCAGGU
..(((.((((((.(.....).))).))).)))..((.((((((((.((((.(((((((((((..(.......)..)).)))......)))))).....)))))))))))).)). ( -33.00)
>consensus
UCCCAUGGGGUUUCCUUUUGAGUCACCUUUGGCUCCCUUUGAGGUUGCUUUUUAGGCUCCCAUUGUGACACUUUUUGUGAAACCUUUGCCUGAUACUUGGGCACCCUUGCAGAU
(((.((((((...(((...((((.(((((.((...))...))))).))))...))).)))))).).)).....((((..(......(((((((...)))))))...)..)))). (-27.00 = -26.75 +  -0.25)

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 10:33:28 2006