Locus 52

Sequence ID 3R_DroMel_CAF1
Location 308,910 – 309,110
Length 200
Max. P 0.982920
window82 window83 window84 window85

overview

Window 2

Location 308,910 – 309,030
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.25
Mean single sequence MFE -42.58
Consensus MFE -34.70
Energy contribution -35.30
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.82
SVM decision value 0.37
SVM RNA-class probability 0.706654
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 308910 120 + 27905053
AGUGACCACCAGUUCGCCAUGAAGUGGAACGUGUACGCAUGGCCGCACCAGAUAAUGGUGCGAUUAUCGACAUUGAAGGACGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCAC
.(((.(((((.(((((((.(.((((.((.((((....))))..(((((((.....)))))))....)).)).)).).)).)))))....))))).....((((....)))))))...... ( -39.30)
>DroSec_CAF1 45312 120 + 1
AGUGACCACCAGUUCGCCAUGAAGUGGAACGUGUAUGCCUGGCCGCACCAGAUAAUGGUGCGGUUAUCCACCUUGAAAGACGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCAC
........(((.(((.....))).)))...(((((.((.(((((((((((.....)))))))))))((((((((.............))))))))......(((.....))))).))))) ( -43.92)
>DroSim_CAF1 46159 120 + 1
AGUGACCACCAGUUCGCCAUGAAGUGGAACGUGUAUGCCUGGCCGCACCAGAUAAUGGUGCGGUUAUCCACCUUGAAAGACGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCAC
........(((.(((.....))).)))...(((((.((.(((((((((((.....)))))))))))((((((((.............))))))))......(((.....))))).))))) ( -43.92)
>DroEre_CAF1 48232 120 + 1
AGUGACCACCAGUUCGCUAUGAAGUGGAACGUGUAUGCGUGGCCCCACCAGAUAAUGGUGCGAUUGUCCACCUUGAAAGACGAGCAGAAGGUGGACAUUGAGGAUUUUCUCCGCCUGCAC
......(((...((((((....))))))..)))..((((.(((..(((((.....)))))((((.(((((((((.............))))))))))))).(((.....)))))))))). ( -39.32)
>DroYak_CAF1 48048 120 + 1
AGUGACCACCAGUUCGCCAUGAAGUGGAACGUGUAUGCAUGGCCGCACCAGAUAAUGGUGCGAUUGUCCACCUUGAAAGACGAGCAGAAGGUGGACAUUGAGGAGUUUCUCCGCCUGCAC
........(((.(((.....))).)))........((((.((((((((((.....)))))))..((((((((((.............))))))))))....((((...))))))))))). ( -46.42)
>consensus
AGUGACCACCAGUUCGCCAUGAAGUGGAACGUGUAUGCAUGGCCGCACCAGAUAAUGGUGCGAUUAUCCACCUUGAAAGACGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCAC
........(((.(((.....))).)))...(((((.((.....(((((((.....)))))))....((((((((.............))))))))......(((.....))))).))))) (-34.70 = -35.30 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 308,910 – 309,030
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.25
Mean single sequence MFE -39.92
Consensus MFE -35.98
Energy contribution -36.18
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.22
Structure conservation index 0.90
SVM decision value 0.27
SVM RNA-class probability 0.662513
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 308910 120 - 27905053
GUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCCUUCAAUGUCGAUAAUCGCACCAUUAUCUGGUGCGGCCAUGCGUACACGUUCCACUUCAUGGCGAACUGGUGGUCACU
(.(((((.((.(...(((...)))...).)).))))).)(.((.(((...((......(((((((.....)))))))((((((((....))........))))))))..))).)).)... ( -34.40)
>DroSec_CAF1 45312 120 - 1
GUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGAUAACCGCACCAUUAUCUGGUGCGGCCAGGCAUACACGUUCCACUUCAUGGCGAACUGGUGGUCACU
((((.(((.(((......)))..((((((((((.............))))))))))..(((((((.....))))))))))..))))....((.(((((....(.....).)))))..)). ( -40.72)
>DroSim_CAF1 46159 120 - 1
GUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGAUAACCGCACCAUUAUCUGGUGCGGCCAGGCAUACACGUUCCACUUCAUGGCGAACUGGUGGUCACU
((((.(((.(((......)))..((((((((((.............))))))))))..(((((((.....))))))))))..))))....((.(((((....(.....).)))))..)). ( -40.72)
>DroEre_CAF1 48232 120 - 1
GUGCAGGCGGAGAAAAUCCUCAAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGACAAUCGCACCAUUAUCUGGUGGGGCCACGCAUACACGUUCCACUUCAUAGCGAACUGGUGGUCACU
((((.((((((.....)))....((((((((((.............))))))))))..(.(((((.....))))).))))..))))....((.(((((............)))))..)). ( -38.02)
>DroYak_CAF1 48048 120 - 1
GUGCAGGCGGAGAAACUCCUCAAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGACAAUCGCACCAUUAUCUGGUGCGGCCAUGCAUACACGUUCCACUUCAUGGCGAACUGGUGGUCACU
((((((((((((...))))....((((((((((.............))))))))))..(((((((.....)))))))))).)))))....((.(((((....(.....).)))))..)). ( -45.72)
>consensus
GUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGAUAAUCGCACCAUUAUCUGGUGCGGCCAGGCAUACACGUUCCACUUCAUGGCGAACUGGUGGUCACU
((((.(((.(((......)))..((((((((((.............))))))))))..(((((((.....))))))))))..))))....((.(((((............)))))..)). (-35.98 = -36.18 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 308,950 – 309,070
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.42
Mean single sequence MFE -46.20
Consensus MFE -40.50
Energy contribution -41.18
Covariance contribution 0.68
Combinations/Pair 1.08
Mean z-score -1.83
Structure conservation index 0.88
SVM decision value 1.93
SVM RNA-class probability 0.982920
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 308950 120 - 27905053
GGGACUCCAGACGCUCCUCGAACGCUUGGCACUCGCUGGCGUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCCUUCAAUGUCGAUAAUCGCACCAUUAUCUGGUGCGGCC
.((((((..(((.((((((..(((((.(((....))))))))...)).))))...)))...)).)))).......(((((.(.......).)))....(((((((.....))))))))). ( -39.30)
>DroSec_CAF1 45352 120 - 1
GGGACUCCAGUCGCUCCUCGAACGCUUGGCACUCGCUGGCGUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGAUAACCGCACCAUUAUCUGGUGCGGCC
((((((....(((((......(((((.(((....))))))))...)))))....))))))...((((((((((.............)))))))))).((((((((.....)))))))).. ( -48.72)
>DroSim_CAF1 46199 120 - 1
GGGACUCCAGUCGCUCCUCGAACGCUUGGCACUCGCUGGCGUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGAUAACCGCACCAUUAUCUGGUGCGGCC
((((((....(((((......(((((.(((....))))))))...)))))....))))))...((((((((((.............)))))))))).((((((((.....)))))))).. ( -48.72)
>DroEre_CAF1 48272 120 - 1
GCGACUCCAGACGCUCCUCAAACGCCUGGCACUCGCUGGAGUGCAGGCGGAGAAAAUCCUCAAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGACAAUCGCACCAUUAUCUGGUGGGGCC
((((((((.((......))....(((((.(((((....))))))))))))))...........((((((((((.............)))))))))).)))).(((((....))))).... ( -47.32)
>DroYak_CAF1 48088 120 - 1
GGGACUCCAGACGCUCCUCAAACGCCUGGCACUCGCUGGCGUGCAGGCGGAGAAACUCCUCAAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGACAAUCGCACCAUUAUCUGGUGCGGCC
((((((((.((......))....(((((.(((.(....).))))))))))))....))))...((((((((((.............)))))))))).((((((((.....)))))))).. ( -46.92)
>consensus
GGGACUCCAGACGCUCCUCGAACGCUUGGCACUCGCUGGCGUGCAGGCGGAGAAAGUCCUCGAUGUCCACCUUCUGCUCGUCUUUCAAGGUGGAUAAUCGCACCAUUAUCUGGUGCGGCC
((((((.......((((((..(((((.(((....))))))))...)).))))..))))))...((((((((((.............)))))))))).((((((((.....)))))))).. (-40.50 = -41.18 +   0.68)

alignment

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secondary structure

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dotplot

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Window 5

Location 308,990 – 309,110
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.42
Mean single sequence MFE -47.21
Consensus MFE -42.24
Energy contribution -42.16
Covariance contribution -0.08
Combinations/Pair 1.06
Mean z-score -1.28
Structure conservation index 0.89
SVM decision value 0.28
SVM RNA-class probability 0.667829
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 308990 120 + 27905053
CGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCACGCCAGCGAGUGCCAAGCGUUCGAGGAGCGUCUGGAGUCCCUCAACGACGAGGUGCAGGCCUACUCACUGGCGUUUAACAC
...(((...((((((..............)))))))))(((((((.((((((((..(((((...)))))..))).(..((((......))))..).....))))).)))))))....... ( -46.74)
>DroSec_CAF1 45392 120 + 1
CGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCACGCCAGCGAGUGCCAAGCGUUCGAGGAGCGACUGGAGUCCCUCAACGACGAGGUGCAGGCCUACUCACUGGCGUUUAAUAC
...(((...((((((..............)))))))))(((((((.(((((((.(((((((...))))).))...(..((((......))))..).)))..)))).)))))))....... ( -45.24)
>DroSim_CAF1 46239 120 + 1
CGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCACGCCAGCGAGUGCCAAGCGUUCGAGGAGCGACUGGAGUCCCUCAACGACGAGGUGCAGGCCUACUCACUGGCGUUUAAUAC
...(((...((((((..............)))))))))(((((((.(((((((.(((((((...))))).))...(..((((......))))..).)))..)))).)))))))....... ( -45.24)
>DroEre_CAF1 48312 120 + 1
CGAGCAGAAGGUGGACAUUGAGGAUUUUCUCCGCCUGCACUCCAGCGAGUGCCAGGCGUUUGAGGAGCGUCUGGAGUCGCUCAACGACGAGGUGCAGGCCUACUCACUGGCGUUUAAUAC
((..(((..(((((.......(((.....)))((((((((..((((((.(.((((((((((...))))))))))).))))).......)..)))))))))))))..))).))........ ( -48.81)
>DroYak_CAF1 48128 120 + 1
CGAGCAGAAGGUGGACAUUGAGGAGUUUCUCCGCCUGCACGCCAGCGAGUGCCAGGCGUUUGAGGAGCGUCUGGAGUCCCUCAACGACGAGGUGCAGGCCUACUCACUGGCGUUUAAUAC
...(((...((((((..............)))))))))(((((((.(((((((((((((((...)))))))))).(..((((......))))..).....))))).)))))))....... ( -50.04)
>consensus
CGAGCAGAAGGUGGACAUCGAGGACUUUCUCCGCCUGCACGCCAGCGAGUGCCAAGCGUUCGAGGAGCGUCUGGAGUCCCUCAACGACGAGGUGCAGGCCUACUCACUGGCGUUUAAUAC
...(((...((((((..............)))))))))(((((((.(((((((.(((((((...))))).))...((.((((......)))).)).)))..)))).)))))))....... (-42.24 = -42.16 +  -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 09:31:28 2006