Locus 6444

Sequence ID 3L_DroMel_CAF1
Location 17,224,822 – 17,224,976
Length 154
Max. P 0.999891
window10343 window10344 window10345 window10346

overview

Window 3

Location 17,224,822 – 17,224,939
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -39.86
Consensus MFE -38.24
Energy contribution -38.28
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -3.50
Structure conservation index 0.96
SVM decision value 4.38
SVM RNA-class probability 0.999885
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17224822 117 + 23771897
CAUUGCUGUUCGGCGGCAGUCAUCGUC---AGAGCUGCACAUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUU
...((((((.(((((((.(((.(((((---((.((.......))....(((........)))........)))))...(((((((......))))))).))))))))))))))))))... ( -43.80)
>DroSec_CAF1 108265 120 + 1
CAUUGCCGUUCGGCGGCAGUCAUCGUCACCAGAGCUGCACAUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUU
...(((.((.(((((((.(((...((((...(.((.......)))...)))).....(((((((((.....((((((.....))))))....))))))))))))))))))))).)))... ( -38.20)
>DroSim_CAF1 101986 120 + 1
CAUUGCCGUUCGGCGGCAGUCAUCGUCACCAGAGCUGCACAUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUU
...(((.((.(((((((.(((...((((...(.((.......)))...)))).....(((((((((.....((((((.....))))))....))))))))))))))))))))).)))... ( -38.20)
>DroEre_CAF1 112008 120 + 1
CAUUGCCGCUCGGCGGCAGUCAUCGUCACCAGAGCUGCACAUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUU
...(((.((.(((((((.(((...((((...(.((.......)))...)))).....(((((((((.....((((((.....))))))....))))))))))))))))))))).)))... ( -40.90)
>DroYak_CAF1 114736 120 + 1
CAUUGCCGUUCGGCGGCAGUCAUCGUCACCAGAGCUGCACAUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUU
...(((.((.(((((((.(((...((((...(.((.......)))...)))).....(((((((((.....((((((.....))))))....))))))))))))))))))))).)))... ( -38.20)
>consensus
CAUUGCCGUUCGGCGGCAGUCAUCGUCACCAGAGCUGCACAUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUU
...(((.((.(((((((.(((...((((...(.((.......)))...)))).....(((((((((.....((((((.....))))))....))))))))))))))))))))).)))... (-38.24 = -38.28 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,224,822 – 17,224,939
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -45.48
Consensus MFE -43.88
Energy contribution -43.92
Covariance contribution 0.04
Combinations/Pair 1.02
Mean z-score -3.66
Structure conservation index 0.96
SVM decision value 4.41
SVM RNA-class probability 0.999891
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17224822 117 - 23771897
AAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAUGUGCAGCUCU---GACGAUGACUGCCGCCGAACAGCAAUG
...(((((.(((((((((((((((....((((((.(((.((((((....))))))...((..((((.....))))..)).))))))))))---)).)).))).)))))))..)))))... ( -43.00)
>DroSec_CAF1 108265 120 - 1
AAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAUGUGCAGCUCUGGUGACGAUGACUGCCGCCGAACGGCAAUG
...(((((.(((((((((((((((....((((((.(((.((((((....))))))...((..((((.....))))..)).)))))))))...))).)).))).)))))))..)))))... ( -44.80)
>DroSim_CAF1 101986 120 - 1
AAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAUGUGCAGCUCUGGUGACGAUGACUGCCGCCGAACGGCAAUG
...(((((.(((((((((((((((....((((((.(((.((((((....))))))...((..((((.....))))..)).)))))))))...))).)).))).)))))))..)))))... ( -44.80)
>DroEre_CAF1 112008 120 - 1
AAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAUGUGCAGCUCUGGUGACGAUGACUGCCGCCGAGCGGCAAUG
...(((((((((((((((((((((....((((((.(((.((((((....))))))...((..((((.....))))..)).)))))))))...))).)).))).))))))).))))))... ( -50.00)
>DroYak_CAF1 114736 120 - 1
AAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAUGUGCAGCUCUGGUGACGAUGACUGCCGCCGAACGGCAAUG
...(((((.(((((((((((((((....((((((.(((.((((((....))))))...((..((((.....))))..)).)))))))))...))).)).))).)))))))..)))))... ( -44.80)
>consensus
AAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAUGUGCAGCUCUGGUGACGAUGACUGCCGCCGAACGGCAAUG
...(((((.(((((((((((((((....((((((.(((.((((((....))))))...((..((((.....))))..)).)))))))))...))).)).))).)))))))..)))))... (-43.88 = -43.92 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,224,859 – 17,224,976
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.15
Mean single sequence MFE -36.06
Consensus MFE -32.78
Energy contribution -33.18
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.91
SVM decision value 2.81
SVM RNA-class probability 0.997191
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17224859 117 + 23771897
AUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUUGGCACCCUGGCACCCAAG---CAGCCUGGCACUUCGGCAC
.((((............(((((((((.....((((((.....))))))....)))))))))......((((((....(((((..(....)...)))))---..))).))).....)))). ( -32.80)
>DroSec_CAF1 108305 120 + 1
AUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUUGGCACCCUGGCACCCAGGCGGCAGCCUGGCACUUCGGCAC
.((((............(((((((((.....((((((.....))))))....)))))))))...((((((((..((.....))...)))))....((((....))))))).....)))). ( -39.20)
>DroSim_CAF1 102026 120 + 1
AUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUUGGCACCCUGGCACCCAGGCGGCAGCCUGGCACUUCGGCAC
.((((............(((((((((.....((((((.....))))))....)))))))))...((((((((..((.....))...)))))....((((....))))))).....)))). ( -39.20)
>DroEre_CAF1 112048 117 + 1
AUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUUGGCACCCUGGCACCCUGG---CAGCCUGGCACUUCGGCAC
.((((............(((((((((.....((((((.....))))))....)))))))))......((((((.((.(..((..(....)..))..))---).))).))).....)))). ( -33.30)
>DroYak_CAF1 114776 117 + 1
AUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUUGGCACCCUGGCACCCAGG---CACCCUGGCACUUUGGCAC
.(((((...........(((((((((.....((((((.....))))))....)))))))))...((((((((......)))))..(((((...)))))---......)))....))))). ( -35.80)
>consensus
AUGCCAUAUGAUUAAUAUUUCAAAAUUACACUGACAUGCAAAGUGUCAACUCAUUUUGAGAGACGCCGCCGGCAGCACUUGGCACCCUGGCACCCAGG___CAGCCUGGCACUUCGGCAC
.((((............(((((((((.....((((((.....))))))....)))))))))...((((((((......)))))..(((((...))))).........))).....)))). (-32.78 = -33.18 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,224,859 – 17,224,976
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.15
Mean single sequence MFE -40.34
Consensus MFE -35.66
Energy contribution -35.54
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.43
Structure conservation index 0.88
SVM decision value 0.48
SVM RNA-class probability 0.752596
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17224859 117 - 23771897
GUGCCGAAGUGCCAGGCUG---CUUGGGUGCCAGGGUGCCAAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAU
(((((((..((((.(((.(---(...((..(....)..))....)).)))...))))..))(((((((..(((((((.......)))))))...)))))))..............))))) ( -40.80)
>DroSec_CAF1 108305 120 - 1
GUGCCGAAGUGCCAGGCUGCCGCCUGGGUGCCAGGGUGCCAAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAU
(((((((..((((.(.(.((.((((.((..(....)..)).)).)).)).).)))))..))(((((((..(((((((.......)))))))...)))))))..............))))) ( -40.80)
>DroSim_CAF1 102026 120 - 1
GUGCCGAAGUGCCAGGCUGCCGCCUGGGUGCCAGGGUGCCAAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAU
(((((((..((((.(.(.((.((((.((..(....)..)).)).)).)).).)))))..))(((((((..(((((((.......)))))))...)))))))..............))))) ( -40.80)
>DroEre_CAF1 112048 117 - 1
GUGCCGAAGUGCCAGGCUG---CCAGGGUGCCAGGGUGCCAAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAU
(((((((..((((.(((.(---((..((..(....)..))..).)).)))...))))..))(((((((..(((((((.......)))))))...)))))))..............))))) ( -40.90)
>DroYak_CAF1 114776 117 - 1
GUGCCAAAGUGCCAGGGUG---CCUGGGUGCCAGGGUGCCAAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAU
((((((..(..((..((..---(....)..))..))..)((((.((((....))))(((.(((.....)))..)))...((((((....)))))).))))..............)))))) ( -38.40)
>consensus
GUGCCGAAGUGCCAGGCUG___CCUGGGUGCCAGGGUGCCAAGUGCUGCCGGCGGCGUCUCUCAAAAUGAGUUGACACUUUGCAUGUCAGUGUAAUUUUGAAAUAUUAAUCAUAUGGCAU
((((((.....(((((......)))))(..(..(.((((.((((((((....))))(((.(((.....)))..))))))).)))).)..)..).....................)))))) (-35.66 = -35.54 +  -0.12)

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 12:19:01 2006