Locus 470

Sequence ID X_DroMel_CAF1
Location 1,384,936 – 1,385,109
Length 173
Max. P 0.951271
window720 window721 window722

overview

Window 0

Location 1,384,936 – 1,385,041
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.40
Mean single sequence MFE -37.90
Consensus MFE -27.28
Energy contribution -28.12
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -2.10
Structure conservation index 0.72
SVM decision value 0.53
SVM RNA-class probability 0.772453
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1384936 105 - 22224390
CACGUUGCUUGCUGCAUGCAGCAUGCUGCAUGAUGCAGCUGG------AGAUUAAAACACGACUUUGAUGCACUGAUGGCGUCUUUGAUUUUAGUCGCUGUC---------GCCUUUCAU
.....(((..(((((((((((....)))))...))))))...------..((((((.......))))))))).(((.((((.(..((((....))))..).)---------)))..))). ( -31.10)
>DroSec_CAF1 12346 114 - 1
CAUGUUGCUUGCUGCAUGCAGCAUGCUGCAUGCUGCAGCUGG------AGAUUAAAACACGACUUUGAUGCACUGAUGGCGUCUUUGAUUUUAGUCGCUGUCGUCGCUGUUGCCUUUCAU
......(((.((.((((((((....)))))))).)))))..(------(((....((((((((...(.....).(((((((.((........)).))))))))))).))))...)))).. ( -39.40)
>DroSim_CAF1 12071 114 - 1
CAUGUUGCUUGCUGCAUGCAGCAUGCUGCAUGCUGCAGCUGG------AGAUUAAAACACGACUUUGAUGCACUGAUGGCGUCUUUGAUUUUAGUCGCUGUCGUCGCUGUUGCCUUUCAU
......(((.((.((((((((....)))))))).)))))..(------(((....((((((((...(.....).(((((((.((........)).))))))))))).))))...)))).. ( -39.40)
>DroEre_CAF1 11313 111 - 1
CUGGCUGCAUGCUGCAUGCUGCAUGCCGCACGCUGCAGCUGG------AGAUUAAAACCCGACUUUGAUGCACAGAUGGCGUCUUUGAUUUUAGUCGCUGUC---GCCGUCGCCUUUCAU
..((((((((((((((.(((((.....))).))))))))(((------..........)))......)))))..(((((((.(..((((....))))..).)---)))))))))...... ( -41.60)
>DroYak_CAF1 591 117 - 1
CAUGUUGAAUGUUGCAUGCUGCAUGCUGCAUGCUGCAGCUGGAGAUGGAGAUUAAAACCCGACUUUGAUGCACAGAUGGCGUCUUUGAUUUUAGUCGCUGUC---GCUGCUGCCUUUCAU
.....((((....((((((........)))))).(((((.((.(((((.((((((((..(((....(((((.(....)))))).))).)))))))).)))))---.)))))))..)))). ( -38.00)
>consensus
CAUGUUGCUUGCUGCAUGCAGCAUGCUGCAUGCUGCAGCUGG______AGAUUAAAACACGACUUUGAUGCACUGAUGGCGUCUUUGAUUUUAGUCGCUGUC___GCUGUUGCCUUUCAU
...(((((.....((((((((....)))))))).)))))..........((((((((..(((....(((((.(....)))))).))).))))))))........................ (-27.28 = -28.12 +   0.84)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,385,001 – 1,385,109
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.08
Mean single sequence MFE -45.88
Consensus MFE -34.59
Energy contribution -35.19
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -2.42
Structure conservation index 0.75
SVM decision value 1.37
SVM RNA-class probability 0.947694
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1385001 108 + 22224390
AGCUGCAUCAUGCAGCAUGCUGCAUGCAGCAAGCAACGUGCAGCGGAGGCUCAACUGCGGAGCGGACAUCAGCG-----------UCCGAAUUUGGUGUGCUGAAUGCAGAAUCCAGA-A
.(((((.....)))))...((((((.(((((.((....(((((..(.....)..)))))...(((((......)-----------))))......)).))))).))))))........-. ( -42.10)
>DroSec_CAF1 12420 108 + 1
AGCUGCAGCAUGCAGCAUGCUGCAUGCAGCAAGCAACAUGCAGCGGAGGCUCAGCUGCGGAGCGGACAUCAGCG-----------UCCGAAUUUGGUGUGCUGAAUGCGGAAUCCAGA-A
.((((((((((((((....)))))))).(....)....))))))(((.((((((((((.((.(((((......)-----------))))...)).))).)))))..))....)))...-. ( -46.50)
>DroSim_CAF1 12145 108 + 1
AGCUGCAGCAUGCAGCAUGCUGCAUGCAGCAAGCAACAUGCAGCGGAGGCUCAGCUGCGGAGCGGACAUCAGCG-----------UCCGAAUUUGGUGUGCUGAAUGCGGAAUCCAGA-A
.((((((((((((((....)))))))).(....)....))))))(((.((((((((((.((.(((((......)-----------))))...)).))).)))))..))....)))...-. ( -46.50)
>DroEre_CAF1 11384 120 + 1
AGCUGCAGCGUGCGGCAUGCAGCAUGCAGCAUGCAGCCAGCAGCCGAGGCUCAACUGCGGAGCGGACAUCAGCGUGCCGCCUCCGUCCGAAUUUGGUGUGCUGAAUGCAGAGUCCCGAAA
..(((((((((((.(((((...))))).))))))...(((((((((((..((....(((((((((.(((....)))))).))))))..)).)))))).)))))..))))).......... ( -52.40)
>DroYak_CAF1 668 119 + 1
AGCUGCAGCAUGCAGCAUGCAGCAUGCAACAUUCAACAUGCAGCGGAGGCUCAACUGCGGAGCGGACAUCAGCGUGCCGCCUCUGUCCGAAUUUGGUGUGCUGAAUGCAGGAUCCAGA-G
..((((((..((.(((.(((.(((((..........))))).)))...))))).)))))).((((.(((....)))))))((((((((..(((..(....)..)))...)))..))))-) ( -41.90)
>consensus
AGCUGCAGCAUGCAGCAUGCUGCAUGCAGCAAGCAACAUGCAGCGGAGGCUCAACUGCGGAGCGGACAUCAGCG___________UCCGAAUUUGGUGUGCUGAAUGCAGAAUCCAGA_A
.((((((((((((((....)))))))).(....)....))))))...((.....(((((...((((((((((....................))))))).)))..)))))...))..... (-34.59 = -35.19 +   0.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,385,001 – 1,385,109
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.08
Mean single sequence MFE -43.78
Consensus MFE -33.75
Energy contribution -34.35
Covariance contribution 0.60
Combinations/Pair 1.07
Mean z-score -2.33
Structure conservation index 0.77
SVM decision value 1.41
SVM RNA-class probability 0.951271
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1385001 108 - 22224390
U-UCUGGAUUCUGCAUUCAGCACACCAAAUUCGGA-----------CGCUGAUGUCCGCUCCGCAGUUGAGCCUCCGCUGCACGUUGCUUGCUGCAUGCAGCAUGCUGCAUGAUGCAGCU
.-.....((.((((((.(((((...(((...((((-----------((....))))))....(((((.(.....).)))))...)))..))))).)))))).))(((((.....))))). ( -38.50)
>DroSec_CAF1 12420 108 - 1
U-UCUGGAUUCCGCAUUCAGCACACCAAAUUCGGA-----------CGCUGAUGUCCGCUCCGCAGCUGAGCCUCCGCUGCAUGUUGCUUGCUGCAUGCAGCAUGCUGCAUGCUGCAGCU
.-...(((....((((.((((...((......)).-----------.))))))))....)))(((((.(.....).))))).....(((.((.((((((((....)))))))).))))). ( -42.90)
>DroSim_CAF1 12145 108 - 1
U-UCUGGAUUCCGCAUUCAGCACACCAAAUUCGGA-----------CGCUGAUGUCCGCUCCGCAGCUGAGCCUCCGCUGCAUGUUGCUUGCUGCAUGCAGCAUGCUGCAUGCUGCAGCU
.-...(((....((((.((((...((......)).-----------.))))))))....)))(((((.(.....).))))).....(((.((.((((((((....)))))))).))))). ( -42.90)
>DroEre_CAF1 11384 120 - 1
UUUCGGGACUCUGCAUUCAGCACACCAAAUUCGGACGGAGGCGGCACGCUGAUGUCCGCUCCGCAGUUGAGCCUCGGCUGCUGGCUGCAUGCUGCAUGCUGCAUGCCGCACGCUGCAGCU
...........((((..((((....(((...((((((((.((((....))).).)))).))))...)))(((....)))))))..)))).((((((.(((((.....))).)))))))). ( -48.30)
>DroYak_CAF1 668 119 - 1
C-UCUGGAUCCUGCAUUCAGCACACCAAAUUCGGACAGAGGCGGCACGCUGAUGUCCGCUCCGCAGUUGAGCCUCCGCUGCAUGUUGAAUGUUGCAUGCUGCAUGCUGCAUGCUGCAGCU
.-..........((((((((((.........((((((..((((...))))..))))))....(((((.(.....).))))).)))))))))).....((((((.((.....)))))))). ( -46.30)
>consensus
U_UCUGGAUUCUGCAUUCAGCACACCAAAUUCGGA___________CGCUGAUGUCCGCUCCGCAGUUGAGCCUCCGCUGCAUGUUGCUUGCUGCAUGCAGCAUGCUGCAUGCUGCAGCU
.....(((....((((.((((..........................))))))))....)))(((((.(.....).)))))..(((((.....((((((((....)))))))).))))). (-33.75 = -34.35 +   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 09:45:20 2006