Locus 4475

Sequence ID 3L_DroMel_CAF1
Location 12,966,803 – 12,966,963
Length 160
Max. P 0.989788
window6976 window6977 window6978

overview

Window 6

Location 12,966,803 – 12,966,923
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.33
Mean single sequence MFE -30.30
Consensus MFE -23.88
Energy contribution -24.04
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -2.76
Structure conservation index 0.79
SVM decision value 2.18
SVM RNA-class probability 0.989788
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12966803 120 + 23771897
UACCUCUGGAUCGCUUCGUUCUGUGUUCGGAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCCCUUGCUUGGCUCAGCUUAGCCAGAGUC
...((((((...(((..(((..(((...((.((..((..(((((((....)))))))..)).(((((.....)))))...........)).))..)))..)))..)))....)))))).. ( -29.20)
>DroSec_CAF1 84042 120 + 1
UACCUCUGGAUCGCUCCAUUCUGCGUUCGUAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCCUUUGCUUGGCUCAGCUUAGCCAGAGUC
...((((((...((((((....(((.((((.....((..(((((((....)))))))..)).(((((.....))))).........)))).....))).)))...)))....)))))).. ( -30.30)
>DroSim_CAF1 88944 120 + 1
UACCUCUGGAUCGCUCCAUUCUGCGUUCGUAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCCCUUGCUUGGCUCAGCUUAGCCAGAGUC
...((((((...((((((....(((.((((.....((..(((((((....)))))))..)).(((((.....))))).........)))).....))).)))...)))....)))))).. ( -30.30)
>DroEre_CAF1 89863 120 + 1
UACCUUUGGAUCGCAGCGUUCUGUUUCCUGCUUCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAUUUCAAACGACUCCAUGCUUAGCUCAACUUAGCCAGAGUC
.......(((..((((.(........))))).)))((..(((((((....)))))))..)).(((((.....)))))...........(((((...(((.((.....)).)))..))))) ( -27.20)
>DroYak_CAF1 87984 120 + 1
UACCUCUGGUUCGCUGCGUUCUGCUUCCUGCUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAUUUCAACCGACUCCUUGCUUAGCUCAGCUCAGCCAGAGUC
...((((((((.((((.(((..((...........((..(((((((....)))))))..)).(((((.....)))))...................))..))).))))..)))))))).. ( -34.50)
>consensus
UACCUCUGGAUCGCUCCGUUCUGCGUUCGGAUCCCUAUUUAAUUAAGCACUUAAUUAUUUAAUGCGCUGAUUGCGCAAUAAUUCAAACGACCCCUUGCUUGGCUCAGCUUAGCCAGAGUC
...((((((...(((..(((..((...........((..(((((((....)))))))..)).(((((.....)))))...................))..)))..)))....)))))).. (-23.88 = -24.04 +   0.16)

alignment

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secondary structure

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Window 7

Location 12,966,803 – 12,966,923
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.33
Mean single sequence MFE -33.76
Consensus MFE -26.44
Energy contribution -27.72
Covariance contribution 1.28
Combinations/Pair 1.06
Mean z-score -2.32
Structure conservation index 0.78
SVM decision value 1.51
SVM RNA-class probability 0.960170
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12966803 120 - 23771897
GACUCUGGCUAAGCUGAGCCAAGCAAGGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUUAAAUAGGGAUCCGAACACAGAACGAAGCGAUCCAGAGGUA
..((((((((......)))).......(((((((((...(((.(((((.....))))).))).(((((((....))))))).......................)))))))))))))... ( -34.10)
>DroSec_CAF1 84042 120 - 1
GACUCUGGCUAAGCUGAGCCAAGCAAAGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUUAAAUAGGGAUACGAACGCAGAAUGGAGCGAUCCAGAGGUA
..((((((((......)))).......((((((((((..(((.(((((.....))))).))).(((((((....)))))))..........)))))((........)))))))))))... ( -35.40)
>DroSim_CAF1 88944 120 - 1
GACUCUGGCUAAGCUGAGCCAAGCAAGGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUUAAAUAGGGAUACGAACGCAGAAUGGAGCGAUCCAGAGGUA
..((((((((......)))).......((((((((((..(((.(((((.....))))).))).(((((((....)))))))..........)))))((........)))))))))))... ( -35.20)
>DroEre_CAF1 89863 120 - 1
GACUCUGGCUAAGUUGAGCUAAGCAUGGAGUCGUUUGAAAUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUUAAAUAGGAAGCAGGAAACAGAACGCUGCGAUCCAAAGGUA
((((((((((.((.....)).))).)))))))........((.(((((.....))))).))..(((((((....)))))))....(((.(((((........).))))..)))....... ( -32.30)
>DroYak_CAF1 87984 120 - 1
GACUCUGGCUGAGCUGAGCUAAGCAAGGAGUCGGUUGAAAUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUUAAAUAGGGAGCAGGAAGCAGAACGCAGCGAACCAGAGGUA
..((((((.(..((((...((((((...(((...((((.....(((((.....)))))))))...)))...))))))............((.....))......))))..)))))))... ( -31.80)
>consensus
GACUCUGGCUAAGCUGAGCCAAGCAAGGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUUAAAUAGGGAUCCGAACGCAGAACGCAGCGAUCCAGAGGUA
..((((((((......)))).......(((((((((....((.(((((.....))))).))..(((((((....))))))).......................)))))))))))))... (-26.44 = -27.72 +   1.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,966,843 – 12,966,963
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -32.24
Consensus MFE -28.72
Energy contribution -28.80
Covariance contribution 0.08
Combinations/Pair 1.15
Mean z-score -1.74
Structure conservation index 0.89
SVM decision value 1.91
SVM RNA-class probability 0.982322
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12966843 120 - 23771897
CUGUCACUACUAUGGUCCACUUUAUAGCUAACUUUCGAAGGACUCUGGCUAAGCUGAGCCAAGCAAGGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUU
..(.((((.((((((......))))))......((((((.((((((((((......))))......)))))).))))))(((.(((((.....))))).))).......)))))...... ( -31.70)
>DroSec_CAF1 84082 120 - 1
CUGUCACUACUAUGGUCCACUCUAUAGCUCACUUUCGAAGGACUCUGGCUAAGCUGAGCCAAGCAAAGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUU
..(.((((.((((((......))))))......((((((.((((((((((......))))......)))))).))))))(((.(((((.....))))).))).......)))))...... ( -33.70)
>DroSim_CAF1 88984 120 - 1
CUGUCACUACUAUGGUCCACUUUAUAGCUCACUUUCGAAGGACUCUGGCUAAGCUGAGCCAAGCAAGGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUU
..(.((((.((((((......))))))......((((((.((((((((((......))))......)))))).))))))(((.(((((.....))))).))).......)))))...... ( -31.70)
>DroEre_CAF1 89903 120 - 1
GUGCCACUACUGAGGUCCACUUUAUAGCUCAAAUUCGAAGGACUCUGGCUAAGUUGAGCUAAGCAUGGAGUCGUUUGAAAUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUU
(..((.(....).))..).......(((.(...((((((.((((((((((.((.....)).))).))))))).)))))).((.(((((.....))))).)).........).)))..... ( -33.90)
>DroYak_CAF1 88024 120 - 1
CUGUCACUACUUGGGUCCACUUUAUAGCUCACAAUCGAAGGACUCUGGCUGAGCUGAGCUAAGCAAGGAGUCGGUUGAAAUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUU
..(.((((...(((((..........)))))...((((..((((((.(((.(((...))).)))..))))))..))))..((.(((((.....))))).))........)))))...... ( -30.20)
>consensus
CUGUCACUACUAUGGUCCACUUUAUAGCUCACUUUCGAAGGACUCUGGCUAAGCUGAGCCAAGCAAGGGGUCGUUUGAAUUAUUGCGCAAUCAGCGCAUUAAAUAAUUAAGUGCUUAAUU
..(.((((.((((((......))))))......((((((.((((((((((......))))......)))))).)))))).((.(((((.....))))).))........)))))...... (-28.72 = -28.80 +   0.08)

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 11:24:13 2006