Locus 4349

Sequence ID 3L_DroMel_CAF1
Location 12,771,890 – 12,772,035
Length 145
Max. P 0.936130
window6731 window6732 window6733

overview

Window 1

Location 12,771,890 – 12,771,997
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 88.50
Mean single sequence MFE -28.96
Consensus MFE -19.02
Energy contribution -18.98
Covariance contribution -0.04
Combinations/Pair 1.26
Mean z-score -3.47
Structure conservation index 0.66
SVM decision value 0.99
SVM RNA-class probability 0.896368
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12771890 107 + 23771897
GGAAUGACUCAAUUUAAUCGCACGGCAAUUUUAUUGACACAAAACUGACAAAACCAAAUGCGAAAAGGAUUAACAUUUCAAAUUUCGCAUUUGUUUUGCAGGCCAGC
((..((..(((((..(((.((...)).)))..)))))..))...(((.((((((.((((((((((..((........))...))))))))))))))))))).))... ( -27.90)
>DroSec_CAF1 13858 107 + 1
GGAAUGACUCAAUUGAAUCGCAUGGGAAUUUAAUUGACACAAAACUGACAAAACCAAAUGCGAAAAGGAUUAACAUUUCCCAUUUCGUAUUUGUUUUGCAGUCCAGC
(((.((..(((((((((((......).))))))))))..))...(((.((((((.((((((((((.(((........)))..))))))))))))))))))))))... ( -31.60)
>DroSim_CAF1 13228 107 + 1
GGAAUGACUCAAUUGAAUCGCAUGGGAAUUUAAUUGACACAAAACUGACAAAAUCAAAUGCGAAAAGGAUUAACAUUUCCCAUUUCGCAUUUGCUUUGCAGUCCAGC
(((.((..(((((((((((......).))))))))))..))...(((.((((..(((((((((((.(((........)))..))))))))))).))))))))))... ( -31.30)
>DroEre_CAF1 12636 107 + 1
GGAAUGACUCAAUUUAUUCGUAUGGGAAUUUAAUUGACACAAAACUGGCGAAACAGAAUGCGAAAAGGAUUAACAUUUUCUAUUUCGCAUUUGUUUUAGAAUCCACC
(((.((..((((((.((((......))))..))))))..))........((((((((.(((((((((((........)))).)))))))))))))))....)))... ( -25.70)
>DroYak_CAF1 12559 107 + 1
GCAAUGACUCAGUUUAUUUGCAUGGGAAUUUAAUUGACACAAAACUGGCAAAACCGAAUGCGAAAAGGAUAAACAUUUUCCAUUUCGCAUUUGUUUUGGAAUGCACC
(((.....(((((((...((((............)).))..)))))))((((((.((((((((((.(((.........))).))))))))))))))))...)))... ( -28.30)
>consensus
GGAAUGACUCAAUUUAAUCGCAUGGGAAUUUAAUUGACACAAAACUGACAAAACCAAAUGCGAAAAGGAUUAACAUUUCCCAUUUCGCAUUUGUUUUGCAGUCCAGC
(((.((..((((((...((......))....))))))..)).......((((((.((((((((((.((...........)).))))))))))))))))...)))... (-19.02 = -18.98 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,771,927 – 12,772,035
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 89.44
Mean single sequence MFE -25.08
Consensus MFE -17.18
Energy contribution -17.14
Covariance contribution -0.04
Combinations/Pair 1.26
Mean z-score -3.56
Structure conservation index 0.69
SVM decision value 1.25
SVM RNA-class probability 0.936130
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12771927 108 + 23771897
CACAAAACUGACAAAACCAAAUGCGAAAAGGAUUAACAUUUCAAAUUUCGCAUUUGUUUUGCAGGCCAGCACAAAGGAAUGUCACUCAAGAUGAUAUAAACAUUUUAA
.......(((.((((((.((((((((((..((........))...))))))))))))))))))).((........)).(((((((....).))))))........... ( -25.40)
>DroSec_CAF1 13895 108 + 1
CACAAAACUGACAAAACCAAAUGCGAAAAGGAUUAACAUUUCCCAUUUCGUAUUUGUUUUGCAGUCCAGCACAAAGGAAUGUCGCUCAAGAUGAUAUAAACAUUUUAA
......((((.((((((.((((((((((.(((........)))..))))))))))))))))))))..((((((......))).))).((((((.......)))))).. ( -27.10)
>DroSim_CAF1 13265 108 + 1
CACAAAACUGACAAAAUCAAAUGCGAAAAGGAUUAACAUUUCCCAUUUCGCAUUUGCUUUGCAGUCCAGCACAAAGGAAUGUCGCUCAAGAUGAUAUAAACAUUUUAA
......((((.((((..(((((((((((.(((........)))..))))))))))).))))))))..((((((......))).))).((((((.......)))))).. ( -26.80)
>DroEre_CAF1 12673 108 + 1
CACAAAACUGGCGAAACAGAAUGCGAAAAGGAUUAACAUUUUCUAUUUCGCAUUUGUUUUAGAAUCCACCACAAAGAAAUGUCGCUCAAUAUGAUAUAAACAUUUUAA
........(((.((((((((.(((((((((((........)))).))))))))))))))).....))).......(((((((...((.....)).....))))))).. ( -19.90)
>DroYak_CAF1 12596 108 + 1
CACAAAACUGGCAAAACCGAAUGCGAAAAGGAUAAACAUUUUCCAUUUCGCAUUUGUUUUGGAAUGCACCAAAAAGUAAUGGCGCUUAAGAUUAUAUAAACAUUUUAA
..((((((.((.....))((((((((((.(((.........))).))))))))))))))))....((.(((........))).))....................... ( -26.20)
>consensus
CACAAAACUGACAAAACCAAAUGCGAAAAGGAUUAACAUUUCCCAUUUCGCAUUUGUUUUGCAGUCCAGCACAAAGGAAUGUCGCUCAAGAUGAUAUAAACAUUUUAA
........(((((....(((((((((((.((...........)).)))))))))))...(((......)))........)))))...((((((.......)))))).. (-17.18 = -17.14 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,771,927 – 12,772,035
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 89.44
Mean single sequence MFE -27.36
Consensus MFE -17.86
Energy contribution -18.46
Covariance contribution 0.60
Combinations/Pair 1.16
Mean z-score -2.57
Structure conservation index 0.65
SVM decision value -0.01
SVM RNA-class probability 0.527642
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12771927 108 - 23771897
UUAAAAUGUUUAUAUCAUCUUGAGUGACAUUCCUUUGUGCUGGCCUGCAAAACAAAUGCGAAAUUUGAAAUGUUAAUCCUUUUCGCAUUUGGUUUUGUCAGUUUUGUG
....((((((....((.....))..)))))).......((..(.(((((((((((((((((((...((........))..)))))))))).)))))).))).)..)). ( -24.00)
>DroSec_CAF1 13895 108 - 1
UUAAAAUGUUUAUAUCAUCUUGAGCGACAUUCCUUUGUGCUGGACUGCAAAACAAAUACGAAAUGGGAAAUGUUAAUCCUUUUCGCAUUUGGUUUUGUCAGUUUUGUG
......((((((........))))))(((......)))((..(((((((((((((((.(((((.((((........))))))))).)))).)))))).)))))..)). ( -26.50)
>DroSim_CAF1 13265 108 - 1
UUAAAAUGUUUAUAUCAUCUUGAGCGACAUUCCUUUGUGCUGGACUGCAAAGCAAAUGCGAAAUGGGAAAUGUUAAUCCUUUUCGCAUUUGAUUUUGUCAGUUUUGUG
......((((((........))))))(((......)))((..(((((((((((((((((((((.((((........))))))))))))))).))))).)))))..)). ( -33.10)
>DroEre_CAF1 12673 108 - 1
UUAAAAUGUUUAUAUCAUAUUGAGCGACAUUUCUUUGUGGUGGAUUCUAAAACAAAUGCGAAAUAGAAAAUGUUAAUCCUUUUCGCAUUCUGUUUCGCCAGUUUUGUG
............(((((((..(((......)))..))))))).........(((((.((((((((((..((((.((.....)).))))))))))))))....))))). ( -23.50)
>DroYak_CAF1 12596 108 - 1
UUAAAAUGUUUAUAUAAUCUUAAGCGCCAUUACUUUUUGGUGCAUUCCAAAACAAAUGCGAAAUGGAAAAUGUUUAUCCUUUUCGCAUUCGGUUUUGCCAGUUUUGUG
.......................((((((........))))))....((((((.(((((((((.(((.........))).))))))))).((.....)).)))))).. ( -29.70)
>consensus
UUAAAAUGUUUAUAUCAUCUUGAGCGACAUUCCUUUGUGCUGGACUGCAAAACAAAUGCGAAAUGGGAAAUGUUAAUCCUUUUCGCAUUUGGUUUUGUCAGUUUUGUG
.(((((((((((........)))))(((.........(((......)))...(((((((((((.(((.........))).))))))))))).....))).)))))).. (-17.86 = -18.46 +   0.60)

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 11:20:17 2006