Locus 4582

Sequence ID 3R_DroMel_CAF1
Location 12,078,583 – 12,078,724
Length 141
Max. P 0.978705
window7521 window7522 window7523 window7524

overview

Window 1

Location 12,078,583 – 12,078,684
Length 101
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.50
Mean single sequence MFE -38.94
Consensus MFE -25.12
Energy contribution -25.76
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.30
Structure conservation index 0.65
SVM decision value 0.28
SVM RNA-class probability 0.664835
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12078583 101 + 27905053
GAAGAGUGGGAGAGCGGG---------U------GGUGCGUCUUCGCCCAUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC----UCGGCCGCUGCGUUUUCGUCU
....(((((..(((((((---------(------((.(((....))))))).((((((.((((..((((.......)))))))).))))))))))----))..)))))(((....))).. ( -40.10)
>DroSec_CAF1 15320 101 + 1
GAAGAGUGGGAGAGCGGG---------U------GGUGCGUCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC----UCGGCCGCUGCGUCUUCGUCU
(((((((((..(((((((---------.------((.(((....)))))))(((((((.((((..((((.......)))))))).))))))))))----))..))))....))))).... ( -39.60)
>DroSim_CAF1 15503 101 + 1
GAAGAGUGGGAGAGCGGG---------U------GGUGCGUCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC----UCGGCCGCUGCGUCUUCGUCU
(((((((((..(((((((---------.------((.(((....)))))))(((((((.((((..((((.......)))))))).))))))))))----))..))))....))))).... ( -39.60)
>DroEre_CAF1 17283 111 + 1
GGAGAGUGGGAGACCGGG---------UGGUGCUGGUGCGUCUUCGCCCCUGCCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGCUCGCUCGGGCGCUUCGUCUUCGUCU
...((((((....))(((---------((((((.((.(((....))).)).))(((((.((((..((((.......)))))))).))))))))))))))))(((((...)))))...... ( -40.60)
>DroYak_CAF1 17572 108 + 1
GAAGAGUGGGAGAGCGGGUAGUGCUGGUGGUGCUGGUGCGUCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCG------------CUUCGUCUUCGUCU
(((((..(((.(.(((((..(..(..(.....)..)..)...)))))))))(((((((.((((..((((.......)))))))).)))))))..------------.....))))).... ( -34.80)
>consensus
GAAGAGUGGGAGAGCGGG_________U______GGUGCGUCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC____UCGGCCGCUGCGUCUUCGUCU
........(((((((((.................((.(((....)))))..(((((((.((((..((((.......)))))))).)))))))..............)))).))))).... (-25.12 = -25.76 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,078,583 – 12,078,684
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.50
Mean single sequence MFE -31.48
Consensus MFE -20.90
Energy contribution -22.14
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -2.19
Structure conservation index 0.66
SVM decision value 0.32
SVM RNA-class probability 0.688965
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12078583 101 - 27905053
AGACGAAAACGCAGCGGCCGA----GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAUGGGCGAAGACGCACC------A---------CCCGCUCUCCCACUCUUC
..........(.((.((..((----(((((((((((.(((((((.......))))..))).)))))))).((((((....))).))------)---------..)))))..)).)))... ( -32.10)
>DroSec_CAF1 15320 101 - 1
AGACGAAGACGCAGCGGCCGA----GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGACGCACC------A---------CCCGCUCUCCCACUCUUC
....(((((....(.((..((----(((((((((((.(((((((.......))))..))).)))))))).((.(((....))).))------.---------..)))))..)).)))))) ( -33.50)
>DroSim_CAF1 15503 101 - 1
AGACGAAGACGCAGCGGCCGA----GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGACGCACC------A---------CCCGCUCUCCCACUCUUC
....(((((....(.((..((----(((((((((((.(((((((.......))))..))).)))))))).((.(((....))).))------.---------..)))))..)).)))))) ( -33.50)
>DroEre_CAF1 17283 111 - 1
AGACGAAGACGAAGCGCCCGAGCGAGCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGGCAGGGGCGAAGACGCACCAGCACCA---------CCCGGUCUCCCACUCUCC
.........((...(((....)))..))((((((((.(((((((.......))))..))).)))))))).((((((....)))...((.(((.---------...))))))))....... ( -28.60)
>DroYak_CAF1 17572 108 - 1
AGACGAAGACGAAG------------CGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGACGCACCAGCACCACCAGCACUACCCGCUCUCCCACUCUUC
....(((((.((((------------(.((((((((.(((((((.......))))..))).)))))))).((((((....)))....((.......))....)))))).))....))))) ( -29.70)
>consensus
AGACGAAGACGCAGCGGCCGA____GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGACGCACC______A_________CCCGCUCUCCCACUCUUC
....(((((...(((((...........((((((((.(((((((.......))))..))).))))))))..(((((....))).)).................))))).......))))) (-20.90 = -22.14 +   1.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,078,608 – 12,078,724
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.77
Mean single sequence MFE -25.83
Consensus MFE -19.26
Energy contribution -19.66
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.75
SVM decision value 0.43
SVM RNA-class probability 0.733170
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12078608 116 + 27905053
UCUUCGCCCAUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC----UCGGCCGCUGCGUUUUCGUCUUCUUCUUAUCCAACUUCGUUGAACCCCAGCUUGCUGGUAA
.....((....(((((((.((((..((((.......)))))))).))))))).))----(((((.((((.(..((((......................))))..)))))..)))))... ( -25.15)
>DroSec_CAF1 15345 116 + 1
UCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC----UCGGCCGCUGCGUCUUCGUCUUCUUCUUAUUCAACUCCGUUGAACCCCAGCUUGCUGGUAA
.....((....(((((((.((((..((((.......)))))))).))))))).))----(((((.((((((....))...........((((((...))))))...))))..)))))... ( -26.10)
>DroSim_CAF1 15528 116 + 1
UCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC----UCGGCCGCUGCGUCUUCGUCUUCUUCUUAUUCAACUCCGUUGAACCCCAGCUUGCUGGUAA
.....((....(((((((.((((..((((.......)))))))).))))))).))----(((((.((((((....))...........((((((...))))))...))))..)))))... ( -26.10)
>DroEre_CAF1 17314 120 + 1
UCUUCGCCCCUGCCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGCUCGCUCGGGCGCUUCGUCUUCGUCUUCUUCUUAUUCAACUCCGUUGAACCCCAGCUCGCUGGUAA
..........((((..(........((((.......)))).((((((((((((((((....)))))....))))))............((((((...))))))....))))))..)))). ( -29.70)
>DroYak_CAF1 17612 107 + 1
UCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCG------------CUUCGUCUUCGUCUUCUUCUUAUUCAACUCCGUUGAAC-CCAGCUUGCUGGUAA
.....((....(((((((.((((..((((.......)))))))).))))))).)------------).....................((((((...)))))).-((((....))))... ( -22.10)
>consensus
UCUUCGCCCCUGUCUUCAAUUCAAUUCAUUUUUAUUAUGAUGAGCUGAAGACCGC____UCGGCCGCUGCGUCUUCGUCUUCUUCUUAUUCAACUCCGUUGAACCCCAGCUUGCUGGUAA
...........(((((((.((((..((((.......)))))))).)))))))....................................((((((...))))))..((((....))))... (-19.26 = -19.66 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,078,608 – 12,078,724
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.77
Mean single sequence MFE -30.72
Consensus MFE -25.17
Energy contribution -25.30
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -2.16
Structure conservation index 0.82
SVM decision value 1.82
SVM RNA-class probability 0.978705
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12078608 116 - 27905053
UUACCAGCAAGCUGGGGUUCAACGAAGUUGGAUAAGAAGAAGACGAAAACGCAGCGGCCGA----GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAUGGGCGAAGA
...((((....)))).(((((((...)))))))................(((.((......----)).((((((((.(((((((.......))))..))).))))))))....))).... ( -30.60)
>DroSec_CAF1 15345 116 - 1
UUACCAGCAAGCUGGGGUUCAACGGAGUUGAAUAAGAAGAAGACGAAGACGCAGCGGCCGA----GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGA
...((((....)))).(((((((...)))))))................(((.((......----)).((((((((.(((((((.......))))..))).))))))))....))).... ( -31.10)
>DroSim_CAF1 15528 116 - 1
UUACCAGCAAGCUGGGGUUCAACGGAGUUGAAUAAGAAGAAGACGAAGACGCAGCGGCCGA----GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGA
...((((....)))).(((((((...)))))))................(((.((......----)).((((((((.(((((((.......))))..))).))))))))....))).... ( -31.10)
>DroEre_CAF1 17314 120 - 1
UUACCAGCGAGCUGGGGUUCAACGGAGUUGAAUAAGAAGAAGACGAAGACGAAGCGCCCGAGCGAGCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGGCAGGGGCGAAGA
...((.((..(((.((((.(..((...(((.............)))...))..).)))).)))..)).((((((((.(((((((.......))))..))).)))))))).))........ ( -34.32)
>DroYak_CAF1 17612 107 - 1
UUACCAGCAAGCUGG-GUUCAACGGAGUUGAAUAAGAAGAAGACGAAGACGAAG------------CGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGA
...((((....))))-(((((((...)))))))................((...------------..((((((((.(((((((.......))))..))).)))))))).....)).... ( -26.50)
>consensus
UUACCAGCAAGCUGGGGUUCAACGGAGUUGAAUAAGAAGAAGACGAAGACGCAGCGGCCGA____GCGGUCUUCAGCUCAUCAUAAUAAAAAUGAAUUGAAUUGAAGACAGGGGCGAAGA
...((((....)))).(((((((...)))))))................(((.((..........)).((((((((.(((((((.......))))..))).))))))))....))).... (-25.17 = -25.30 +   0.13)

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 11:33:37 2006