Locus 2951

Sequence ID X_DroMel_CAF1
Location 7,897,407 – 7,897,567
Length 160
Max. P 0.794478
window4843 window4844 window4845

overview

Window 3

Location 7,897,407 – 7,897,527
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -48.13
Consensus MFE -45.93
Energy contribution -46.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.95
SVM decision value 0.60
SVM RNA-class probability 0.794478
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7897407 120 + 22224390
CUCCUGCUGCUGUCACACCGGCACCAAAGCCAGCACCGGCCGCGGCACCGCCGCCCGCCAUCUGGCUAAAGGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAA
.......(((.........(((......))).((((.(((((((((...)))))..(((....)))....))))..(((((.((.....)).)))))))))...)))(((.....))).. ( -46.10)
>DroSim_CAF1 1141 120 + 1
CUCCAGCUGCUGUCACACCGGCACCAAAGCCAGCACCGGCCGCGGCACCGCCGCCCGCCAGCUGGCUAAAGGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAA
...((((((...((((..((.......(((((((...(((.(((((...)))))..))).)))))))...(((....))).))..))))...)))))).........(((.....))).. ( -49.30)
>DroYak_CAF1 1142 120 + 1
CUCCUGCUGCUGUCACACCGGCACCAAAGCCAGCACCGGCCGCGGCACCGCCGCCCGCCAGCUGGCUAAAUGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAA
....(((.(.((.(((...((((....(((((((...(((.(((((...)))))..))).)))))))...))))..(((((.((.....)).)))))))))).))))(((.....))).. ( -49.00)
>consensus
CUCCUGCUGCUGUCACACCGGCACCAAAGCCAGCACCGGCCGCGGCACCGCCGCCCGCCAGCUGGCUAAAGGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAA
.....((.(.((.(((...(((.....(((((((...(((.(((((...)))))..))).)))))))....)))..(((((.((.....)).)))))))))).))).(((.....))).. (-45.93 = -46.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,897,407 – 7,897,527
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -60.70
Consensus MFE -57.33
Energy contribution -58.00
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.94
SVM decision value 0.60
SVM RNA-class probability 0.794080
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7897407 120 - 22224390
UUCCCAAUGUGGGUGCGUUGCACAGCCAGGUUCACGACGUGGCCAUGGCCUUUAGCCAGAUGGCGGGCGGCGGUGCCGCGGCCGGUGCUGGCUUUGGUGCCGGUGUGACAGCAGCAGGAG
..(((.....)))(((((..(((.((((.(((...))).))))..((((((..((((((...((.(((.(((....))).))).)).))))))..)).)))))))..)).)))....... ( -58.70)
>DroSim_CAF1 1141 120 - 1
UUCCCAAUGUGGGUGCGUUGCACAGCCAGGUUCACGACGUGGCCAUGGCCUUUAGCCAGCUGGCGGGCGGCGGUGCCGCGGCCGGUGCUGGCUUUGGUGCCGGUGUGACAGCAGCUGGAG
.(((......((.(((((..(((.((((.(((...))).))))..((((((..(((((((..((.(((.(((....))).))).)))))))))..)).)))))))..)).))).))))). ( -61.50)
>DroYak_CAF1 1142 120 - 1
UUCCCAAUGUGGGUGCGUUGCACAGCCAGGUUCACGACGUGGCCAUGGCAUUUAGCCAGCUGGCGGGCGGCGGUGCCGCGGCCGGUGCUGGCUUUGGUGCCGGUGUGACAGCAGCAGGAG
..(((.....)))(((((..(((.((((.(((...))).))))..(((((((.(((((((..((.(((.(((....))).))).)))))))))..))))))))))..)).)))....... ( -61.90)
>consensus
UUCCCAAUGUGGGUGCGUUGCACAGCCAGGUUCACGACGUGGCCAUGGCCUUUAGCCAGCUGGCGGGCGGCGGUGCCGCGGCCGGUGCUGGCUUUGGUGCCGGUGUGACAGCAGCAGGAG
..(((.....)))(((((..(((.((((.(((...))).))))..((((((..(((((((..((.(((.(((....))).))).)))))))))..)).)))))))..)).)))....... (-57.33 = -58.00 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,897,447 – 7,897,567
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -49.00
Consensus MFE -46.94
Energy contribution -46.83
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.96
SVM decision value -0.02
SVM RNA-class probability 0.521856
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7897447 120 + 22224390
CGCGGCACCGCCGCCCGCCAUCUGGCUAAAGGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAACGCCUCCUGCGACGGCCGCUCCGCCAUGGCCAACCAAUGA
.(((((...)))))..(((....)))....((((((((((((...))).....(((((((((..((.(((.....)))...))....))).)))))).....)))))))))......... ( -50.40)
>DroSim_CAF1 1181 120 + 1
CGCGGCACCGCCGCCCGCCAGCUGGCUAAAGGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAACGCCUCCUGCGACGGCCGCUCCGCCAUGGCCAACCAAUGA
.(((((...)))))..(((....)))....((((((((((((...))).....(((((((((..((.(((.....)))...))....))).)))))).....)))))))))......... ( -50.40)
>DroYak_CAF1 1182 120 + 1
CGCGGCACCGCCGCCCGCCAGCUGGCUAAAUGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAACGCCGCCUGCGAUGGCUGCUCCGCCAUGGCCAACCAACGA
.(((((...)))))..((((..((((.....))))))))....((((.....((((((((....((.(((.....)))...((.(((......))).))...))))))))))....)))) ( -46.20)
>consensus
CGCGGCACCGCCGCCCGCCAGCUGGCUAAAGGCCAUGGCCACGUCGUGAACCUGGCUGUGCAACGCACCCACAUUGGGAACGCCUCCUGCGACGGCCGCUCCGCCAUGGCCAACCAAUGA
.(((((...)))))..(((....)))....((((((((((((...))).....(((((((((..((.(((.....)))...))....))).)))))).....)))))))))......... (-46.94 = -46.83 +  -0.11)

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 10:47:34 2006