Locus 4988

Sequence ID 3L_DroMel_CAF1
Location 13,747,812 – 13,748,039
Length 227
Max. P 0.999798
window7875 window7876 window7877 window7878 window7879

overview

Window 5

Location 13,747,812 – 13,747,924
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 90.89
Mean single sequence MFE -34.36
Consensus MFE -30.46
Energy contribution -30.30
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.27
Structure conservation index 0.89
SVM decision value 0.25
SVM RNA-class probability 0.653984
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13747812 112 - 23771897
CACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAGCAUAGACUAACUGAACGAAAGCUGAAGUUGUCCCGCCUCCAAAGAGAAGGCGGAAGUUGGCCA
...(((((...(((((.....)))))...)))))...((((((..........(((.((((..((....).)..)))))))((((((.(.....).))))))..)))))).. ( -37.80)
>DroSec_CAF1 154555 99 - 1
CACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAG-------------AACGAAAGCUGAAAUCGACCCGCCUCCAAAGCGAAGGCGGAAGUUGGCCA
...(((((...(((((.....)))))...)))))...((((((.(((..-------------..(....))))........((((((.(.....).))))))..)))))).. ( -32.90)
>DroSim_CAF1 166198 112 - 1
CACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAGCAUAGUCUAACUGAACGAAAGCUGAAGUCGACCCGCCUCCAAAGCGAAGGCGGAAGUUGGCCA
......(((((....)))))(((((((.(((.....(((....))).))).)))))))......(....).....((((((((((((.(.....).))))))..)))))).. ( -35.60)
>DroEre_CAF1 161416 112 - 1
CACUCCGGAGGAGUCCUUCCUGGACUGAGUUAUAAAUGCCAACGCAGAGCAUAGUCUAACUUAACGAAAGCUGAAGUCGUCCCGCCUCCAAAGCGAAGGCGGAAGUUGGCCA
((.((((((((....))))).))).))..........((((((...............((((..(....)...))))....((((((.(.....).))))))..)))))).. ( -33.60)
>DroYak_CAF1 165693 112 - 1
CACUGUGGAGGAGUCCUUCCUGGACUGAGUUAUAAAUGCCAACGCAGAGCAUAGUCUAACUGAACGAAAGCCGAAGUCGUCCCGCCACCAAAGCGAUGGCGGAAGUUGGCCA
......(((((....)))))(((((((.(((.....(((....))).))).)))))))...........(((((.......((((((.(.....).))))))...))))).. ( -31.90)
>consensus
CACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAGCAUAGUCUAACUGAACGAAAGCUGAAGUCGUCCCGCCUCCAAAGCGAAGGCGGAAGUUGGCCA
...(((((...(((((.....)))))...)))))...((((((.....................(....)...........((((((.(.....).))))))..)))))).. (-30.46 = -30.30 +  -0.16)

alignment

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secondary structure

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Window 6

Location 13,747,851 – 13,747,964
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -23.76
Consensus MFE -19.62
Energy contribution -19.78
Covariance contribution 0.16
Combinations/Pair 1.05
Mean z-score -1.42
Structure conservation index 0.83
SVM decision value 0.15
SVM RNA-class probability 0.609204
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13747851 113 - 23771897
CGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAGCAUAGACUAACUGAACGAAAGCUG
...........(((.........((((.....((((((........))))))((((.....)))))))).......(((....))))))...............(....)... ( -21.40)
>DroSec_CAF1 154594 100 - 1
CGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAG-------------AACGAAAGCUG
...........(((.........((((.....((((((........))))))((((.....)))))))).......(((....))))))-------------..(....)... ( -22.10)
>DroSim_CAF1 166237 113 - 1
CGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAGCAUAGUCUAACUGAACGAAAGCUG
..................................(((((((.....)))))))((.(((.(((((((.(((.....(((....))).))).)))))))...))).))...... ( -24.50)
>DroEre_CAF1 161455 113 - 1
CGACCAACCCACUCAUACACUCCCUCAACACUCCCUCCUCCACUCCGGAGGAGUCCUUCCUGGACUGAGUUAUAAAUGCCAACGCAGAGCAUAGUCUAACUUAACGAAAGCUG
.(((......(((((....................((((((.....))))))((((.....))))))))).....(((((......).)))).)))........(....)... ( -25.50)
>DroYak_CAF1 165732 106 - 1
CGACCAACCCACUCAUACACCCCC-------UCCCUCCUUCACUGUGGAGGAGUCCUUCCUGGACUGAGUUAUAAAUGCCAACGCAGAGCAUAGUCUAACUGAACGAAAGCCG
.(((......((((..........-------..(((((........)))))(((((.....))))))))).....(((((......).)))).)))........(....)... ( -25.30)
>consensus
CGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAUAAAUGCCAACGCAGAGCAUAGUCUAACUGAACGAAAGCUG
...........(((.........(((.......(((((........)))))(((((.....)))))))).......(((....))))))...............(....)... (-19.62 = -19.78 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,747,891 – 13,747,999
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 93.52
Mean single sequence MFE -31.16
Consensus MFE -27.28
Energy contribution -26.64
Covariance contribution -0.64
Combinations/Pair 1.11
Mean z-score -1.61
Structure conservation index 0.88
SVM decision value 1.33
SVM RNA-class probability 0.943317
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13747891 108 + 23771897
AUAGCUCAGUCCAGGAAGGACUCCUCCACAGUGGAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGGGCAAU
...(((((((((.....)))))((((.(((.(.........).))).))))..(((.((...((.((..(((((......)))))..)).)).)))))...))))... ( -31.50)
>DroSec_CAF1 154621 108 + 1
AUAGCUCAGUCCAGGAAGGACUCCUCCACAGUGGAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGGGCAAU
...(((((((((.....)))))((((.(((.(.........).))).))))..(((.((...((.((..(((((......)))))..)).)).)))))...))))... ( -31.50)
>DroSim_CAF1 166277 108 + 1
AUAGCUCAGUCCAGGAAGGACUCCUCCACAGUGGAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAAGGCAAU
...(((((((((.....)))))((((.(((.(.........).))).))))))))...(((....((..(((((......)))))..)).....)))........... ( -29.80)
>DroEre_CAF1 161495 108 + 1
AUAACUCAGUCCAGGAAGGACUCCUCCGGAGUGGAGGAGGGAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGGGCAAU
....(((..(((....((.((((((((........))).))))).))...)))(((.((...((.((..(((((......)))))..)).)).))))).)))...... ( -32.30)
>DroYak_CAF1 165772 101 + 1
AUAACUCAGUCCAGGAAGGACUCCUCCACAGUGAAGGAGGGA-------GGGGGUGUAUGAGUGGGUUGGUCGUCUGAGAGUGACUGGCAUAAAUCACAGAGGGCAAU
.(((((((((((.....))))((((((........)))))).-------.............)))))))(((.((((.(((((.....)))...)).)))).)))... ( -30.70)
>consensus
AUAGCUCAGUCCAGGAAGGACUCCUCCACAGUGGAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGGGCAAU
.(((((((((((.....))))(((((..........))))).....................)))))))(((.((((.(((((.....)))...)).)))).)))... (-27.28 = -26.64 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,747,891 – 13,747,999
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 93.52
Mean single sequence MFE -22.34
Consensus MFE -22.42
Energy contribution -21.86
Covariance contribution -0.56
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 1.00
SVM decision value 4.10
SVM RNA-class probability 0.999798
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13747891 108 - 23771897
AUUGCCCUCUGUGAUUUAUGCCAGUCAUUCUCAGACGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAU
.(((..((((((((((......)))))....)))).)..)))................((((.....((((((........))))))((((.....)))))))).... ( -21.20)
>DroSec_CAF1 154621 108 - 1
AUUGCCCUCUGUGAUUUAUGCCAGUCAUUCUCAGACGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAU
.(((..((((((((((......)))))....)))).)..)))................((((.....((((((........))))))((((.....)))))))).... ( -21.20)
>DroSim_CAF1 166277 108 - 1
AUUGCCUUCUGUGAUUUAUGCCAGUCAUUCUCAGACGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAU
..........((((((......)))))).(((((...................................(((((((.....)))))))(((.....)))))))).... ( -20.90)
>DroEre_CAF1 161495 108 - 1
AUUGCCCUCUGUGAUUUAUGCCAGUCAUUCUCAGACGACCAACCCACUCAUACACUCCCUCAACACUCCCUCCUCCACUCCGGAGGAGUCCUUCCUGGACUGAGUUAU
.(((..((((((((((......)))))....)))).)..)))...(((((....................((((((.....))))))((((.....)))))))))... ( -24.20)
>DroYak_CAF1 165772 101 - 1
AUUGCCCUCUGUGAUUUAUGCCAGUCACUCUCAGACGACCAACCCACUCAUACACCCCC-------UCCCUCCUUCACUGUGGAGGAGUCCUUCCUGGACUGAGUUAU
..........((((((......)))))).................((((..........-------..(((((........)))))(((((.....)))))))))... ( -24.20)
>consensus
AUUGCCCUCUGUGAUUUAUGCCAGUCAUUCUCAGACGACCAACCCACUCAUACACUCCCUCAACACUUCCUCUUCCACUGUGGAGGAGUCCUUCCUGGACUGAGCUAU
..........((((((......)))))).(((((...................................(((((((.....)))))))(((.....)))))))).... (-22.42 = -21.86 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,747,924 – 13,748,039
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.81
Mean single sequence MFE -35.08
Consensus MFE -22.81
Energy contribution -23.87
Covariance contribution 1.06
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.65
SVM decision value 0.25
SVM RNA-class probability 0.652145
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13747924 115 + 23771897
GAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGG-----GCAAUAUGCAACACUAUUUCCAGUACGGCACUGCAAAUACUCCUC
...(((((.(((((...(.(((((...(.(((((..(((((......)))))..))..............-----((.....))..........))).)...))))).).)))))))))) ( -35.50)
>DroSec_CAF1 154654 115 + 1
GAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGG-----GCAAUAUGCAACACUAUUUCCAGUGCGGCACUGCAAAUACUCCUC
...(((((.(((((...(.(((((...(.(((((..(((((......)))))..))..............-----((.....))..........))).)...))))).).)))))))))) ( -34.40)
>DroSim_CAF1 166310 115 + 1
GAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAAG-----GCAAUAUGCAACACUAUUUCCAGUGCGGCACUGCAAAUACUCCUC
...(((((.(((((...(.(((((...(.(((((..(((((......)))))..))..............-----((.....))..........))).)...))))).).)))))))))) ( -34.40)
>DroEre_CAF1 161528 115 + 1
GAGGAGGGAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGG-----GCAAUAUGCAACACUAUUUCCAGAGCGGCACUGCAAAUACUCCUC
(((((((.(((((((..((((......((((.((..(((((......)))))..))..............-----((.....))..))))..))))....))))))).).....)))))) ( -36.50)
>DroYak_CAF1 165805 108 + 1
AAGGAGGGA-------GGGGGUGUAUGAGUGGGUUGGUCGUCUGAGAGUGACUGGCAUAAAUCACAGAGG-----GCAAUAUGCAACACUAUUUCCAGUGCGGCACUGCAAAUACUCCUG
.((((((((-------((.(((((.(((....((..((((........))))..)).....)))......-----((.....)).))))).)))))..((((....))))....))))). ( -33.30)
>DroPer_CAF1 158330 101 + 1
-------CA-------CAAUGUG----CUUGGGUGGGUGGUGC-CGAGUGACUGGCAUAAAUCACUGGGCGCCACGCAGUAUGCAACAUUAUUUUUAGUUCAGCAUUGUAAAUACUCGCU
-------.(-------(((((((----(...(.((.(((((((-(.(((((.(......).))))).)))))))).)).)..))...((((....))))...)))))))........... ( -36.40)
>consensus
GAAGAGGAAGUGUUGAGGGAGUGUAUGAGUGGGUUGGUCGUCUGAGAAUGACUGGCAUAAAUCACAGAGG_____GCAAUAUGCAACACUAUUUCCAGUGCGGCACUGCAAAUACUCCUC
................((((((((....((((((..(((((......)))))..)).....))))..........(((...(((..((((......))))..))).)))..)))))))). (-22.81 = -23.87 +   1.06)

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 11:38:47 2006