Locus 144

Sequence ID 2R_DroMel_CAF1
Location 1,404,968 – 1,405,159
Length 191
Max. P 0.893374
window323 window324 window325 window326

overview

Window 3

Location 1,404,968 – 1,405,088
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.25
Mean single sequence MFE -41.77
Consensus MFE -32.73
Energy contribution -32.40
Covariance contribution -0.33
Combinations/Pair 1.11
Mean z-score -1.98
Structure conservation index 0.78
SVM decision value 0.25
SVM RNA-class probability 0.651035
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1404968 120 + 20766785
UCAGCUGGCUUCAGUUGGCGGUGUGAUGCCGAAGCCUCCUGACUUUGGGGUAGAGAACUGCAAGCUGCGGACUGCAAGCUGCGAACUGCAAACUGCAAACUACUAGCAGCUAGCUGCAAG
.((((((((..(((((.(((((.((...(((.(((..(((......)))((((....))))..))).)))....)).))))).))))).....(((.........))))))))))).... ( -44.00)
>DroSec_CAF1 30802 109 + 1
UCAGCUGCCUCCAGUUGGCG----GAUGCCGAAGCCUCCUCACUUCGGAGUAGAGAACUGCUAGCUGCGAACUGCAAACUGCAAACUGCAAACU-------GCUAGCUGCUAGCUGCUAG
.((((((....(((((((((----(...((((((........))))))(((((....)))))...((((...(((.....)))...))))..))-------)))))))).)))))).... ( -38.40)
>DroSim_CAF1 35811 109 + 1
UCAGCUGGCUCCAGUUGGCG----GAUGCCGAAGCCUCCUCACUUCGGAGUGGAGAACUGCUAGCUGCGAACUGCAAACUGCAAACUGCAAACU-------GCUAGCUGCUAGCUGCUAG
.(((((((((((((((((((----(..((....))((((.(.(....).).))))..)))))))))).)).(((((...(((.....)))...)-------)).))..)))))))).... ( -42.90)
>consensus
UCAGCUGGCUCCAGUUGGCG____GAUGCCGAAGCCUCCUCACUUCGGAGUAGAGAACUGCUAGCUGCGAACUGCAAACUGCAAACUGCAAACU_______GCUAGCUGCUAGCUGCUAG
.((((((((..(((((.((.........((((((........)))))).((((....)))).....)).))))).....(((.....)))..................)))))))).... (-32.73 = -32.40 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,404,968 – 1,405,088
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.25
Mean single sequence MFE -41.73
Consensus MFE -32.05
Energy contribution -32.50
Covariance contribution 0.45
Combinations/Pair 1.09
Mean z-score -1.84
Structure conservation index 0.77
SVM decision value 0.03
SVM RNA-class probability 0.550755
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1404968 120 - 20766785
CUUGCAGCUAGCUGCUAGUAGUUUGCAGUUUGCAGUUCGCAGCUUGCAGUCCGCAGCUUGCAGUUCUCUACCCCAAAGUCAGGAGGCUUCGGCAUCACACCGCCAACUGAAGCCAGCUGA
....(((((((((((.(((.((((((((.((((.....)))).))))))...)).))).))))))...................(((((((((........)))....))))))))))). ( -40.20)
>DroSec_CAF1 30802 109 - 1
CUAGCAGCUAGCAGCUAGC-------AGUUUGCAGUUUGCAGUUUGCAGUUCGCAGCUAGCAGUUCUCUACUCCGAAGUGAGGAGGCUUCGGCAUC----CGCCAACUGGAGGCAGCUGA
....(((((.((.((((((-------...((((.....))))..(((.....))))))))).........(((((...((.(((.((....)).))----)..))..)))))))))))). ( -42.90)
>DroSim_CAF1 35811 109 - 1
CUAGCAGCUAGCAGCUAGC-------AGUUUGCAGUUUGCAGUUUGCAGUUCGCAGCUAGCAGUUCUCCACUCCGAAGUGAGGAGGCUUCGGCAUC----CGCCAACUGGAGCCAGCUGA
.((((.((((((((((.((-------((.((((.....)))).))))))))....))))))...((..((((....))))..))(((((((((...----.)))....)))))).)))). ( -42.10)
>consensus
CUAGCAGCUAGCAGCUAGC_______AGUUUGCAGUUUGCAGUUUGCAGUUCGCAGCUAGCAGUUCUCUACUCCGAAGUGAGGAGGCUUCGGCAUC____CGCCAACUGGAGCCAGCUGA
....(((((....((((((..........((((.....))))..(((.....)))))))))...(((.(((......))).)))(((((((((........)))....))))))))))). (-32.05 = -32.50 +   0.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,405,048 – 1,405,159
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.91
Mean single sequence MFE -40.33
Consensus MFE -31.93
Energy contribution -33.27
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.79
SVM decision value 0.98
SVM RNA-class probability 0.893374
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1405048 111 + 20766785
GCGAACUGCAAACUGCAAACUACUAGCAGCUAGCUGCAAGC-UGCUAACUGCGAGUGGCAUCAGCGUCAUCGCCUGACGCUGACUGGUGGCCCUAACG---CACACAUUCAGCC-----A
(((...(((.....)))......((((((((.......)))-)))))..)))...((((.(((((((((.....)))))))))...(((((......)---).))).....)))-----) ( -40.20)
>DroSec_CAF1 30878 104 + 1
GCAAACUGCAAACU-------GCUAGCUGCUAGCUGCUAGCUUGCUAACUGCGAGUGGCAUCAGCGUCAUCGCUUGACGCUGACUGGUGGCCCCAACGACGCACGCA----GCC-----A
((.....))...((-------((..((..((((.(((((.(((((.....))))))))))(((((((((.....)))))))))))))..))......(.....))))----)..-----. ( -41.20)
>DroSim_CAF1 35887 113 + 1
GCAAACUGCAAACU-------GCUAGCUGCUAGCUGCUAGCUUGCUAACUGCGAGUGGCAUCAGCGUCAUCGCCUGACGCGGACUGGUGGCCCCAACGACGCACACAUUCAGCCAGCCAA
(((....((((...-------((((((........))))))))))....)))...((((....((((((.....))))))((.((((((((.........)).)))...))))).)))). ( -39.60)
>consensus
GCAAACUGCAAACU_______GCUAGCUGCUAGCUGCUAGCUUGCUAACUGCGAGUGGCAUCAGCGUCAUCGCCUGACGCUGACUGGUGGCCCCAACGACGCACACAUUCAGCC_____A
((.....))................((((((((.(((((.(((((.....))))))))))(((((((((.....)))))))))))))))))............................. (-31.93 = -33.27 +   1.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,405,048 – 1,405,159
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.91
Mean single sequence MFE -46.77
Consensus MFE -34.39
Energy contribution -35.83
Covariance contribution 1.45
Combinations/Pair 1.03
Mean z-score -2.39
Structure conservation index 0.74
SVM decision value 0.91
SVM RNA-class probability 0.880644
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1405048 111 - 20766785
U-----GGCUGAAUGUGUG---CGUUAGGGCCACCAGUCAGCGUCAGGCGAUGACGCUGAUGCCACUCGCAGUUAGCA-GCUUGCAGCUAGCUGCUAGUAGUUUGCAGUUUGCAGUUCGC
(-----((((.((((....---))))..)))))...((((((((((.....))))))))))((.(((.(((((((((.-.......))))))))).))).))((((.....))))..... ( -45.80)
>DroSec_CAF1 30878 104 - 1
U-----GGC----UGCGUGCGUCGUUGGGGCCACCAGUCAGCGUCAAGCGAUGACGCUGAUGCCACUCGCAGUUAGCAAGCUAGCAGCUAGCAGCUAGC-------AGUUUGCAGUUUGC
(-----(((----((((.((((((((((.....)))).)(((((((.....))))))))))))....))))))))(((((((.(((((.....))).))-------)))))))....... ( -45.80)
>DroSim_CAF1 35887 113 - 1
UUGGCUGGCUGAAUGUGUGCGUCGUUGGGGCCACCAGUCCGCGUCAGGCGAUGACGCUGAUGCCACUCGCAGUUAGCAAGCUAGCAGCUAGCAGCUAGC-------AGUUUGCAGUUUGC
...((((((((...(((.(((((....((((.....))))((((((.....)))))).))))))))...))))))))..((((((........))))))-------.............. ( -48.70)
>consensus
U_____GGCUGAAUGUGUGCGUCGUUGGGGCCACCAGUCAGCGUCAGGCGAUGACGCUGAUGCCACUCGCAGUUAGCAAGCUAGCAGCUAGCAGCUAGC_______AGUUUGCAGUUUGC
......(((....((.(((.(((.....))))))))((((((((((.....)))))))))))))....((((...(((((((....(((((...))))).......)))))))...)))) (-34.39 = -35.83 +   1.45)

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 09:29:49 2006