Locus 5921

Sequence ID X_DroMel_CAF1
Location 15,275,759 – 15,275,888
Length 129
Max. P 0.996274
window9611 window9612 window9613

overview

Window 1

Location 15,275,759 – 15,275,857
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 82.76
Mean single sequence MFE -34.47
Consensus MFE -29.66
Energy contribution -30.33
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -2.37
Structure conservation index 0.86
SVM decision value 1.66
SVM RNA-class probability 0.970762
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15275759 98 + 22224390
GAGCCGAAAGGACACUACUACUGCUCCUCAGGCGGAACAGCCCGCUGGGAAAUGGAGCAGUAGUGUCCGGGUUUUUGUUUUUUUGUGGGGCGGGGAUC
.........(((((((...((((((((((.(((((......)))))..))...))))))))))))))).((((((((((((.....)))))))))))) ( -40.70)
>DroSec_CAF1 99692 94 + 1
GAGCCGAAAGGACACUACUACUGCUCCUCAGGCGGAACAGCCCGCUGGGAAAUGGAGCAGUAGUGUCCGGGUUUUUUUUUUUU----GGGAGGGAAUC
(((((....(((((((...((((((((((.(((((......)))))..))...))))))))))))))).)))))(((((((..----..))))))).. ( -38.00)
>DroYak_CAF1 87958 87 + 1
GAGCCGAAAGGACACUACAACUGCUCCUUAGGCGAAACAGCCCGUUGGGAAAUGGAGCAAUAGUAUUCGGGUAUUUU-----U----GGCA--AAUUC
..((((((((.((..(((...((((((...(((......))).(((....)))))))))...))).....)).))))-----)----))).--..... ( -24.70)
>consensus
GAGCCGAAAGGACACUACUACUGCUCCUCAGGCGGAACAGCCCGCUGGGAAAUGGAGCAGUAGUGUCCGGGUUUUUUUUUUUU____GGGAGGGAAUC
(((((....(((((((((...((((((((.(((((......)))))..))...))))))))))))))).)))))........................ (-29.66 = -30.33 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,275,759 – 15,275,857
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 82.76
Mean single sequence MFE -29.65
Consensus MFE -27.67
Energy contribution -28.23
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -2.79
Structure conservation index 0.93
SVM decision value 2.68
SVM RNA-class probability 0.996274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15275759 98 - 22224390
GAUCCCCGCCCCACAAAAAAACAAAAACCCGGACACUACUGCUCCAUUUCCCAGCGGGCUGUUCCGCCUGAGGAGCAGUAGUAGUGUCCUUUCGGCUC
.......(((....................(((((((((((((....(((((((((((....)))).))).)))).)))))))))))))....))).. ( -33.95)
>DroSec_CAF1 99692 94 - 1
GAUUCCCUCCC----AAAAAAAAAAAACCCGGACACUACUGCUCCAUUUCCCAGCGGGCUGUUCCGCCUGAGGAGCAGUAGUAGUGUCCUUUCGGCUC
...........----...............(((((((((((((....(((((((((((....)))).))).)))).)))))))))))))......... ( -33.70)
>DroYak_CAF1 87958 87 - 1
GAAUU--UGCC----A-----AAAAUACCCGAAUACUAUUGCUCCAUUUCCCAACGGGCUGUUUCGCCUAAGGAGCAGUUGUAGUGUCCUUUCGGCUC
.....--.(((----.-----(((..((.....(((.((((((((.((.......((((......)))))))))))))).)))..))..))).))).. ( -21.31)
>consensus
GAUUCCCUCCC____AAAAAAAAAAAACCCGGACACUACUGCUCCAUUUCCCAGCGGGCUGUUCCGCCUGAGGAGCAGUAGUAGUGUCCUUUCGGCUC
..............................(((((((((((((....((((...(((((......))))).)))).)))))))))))))......... (-27.67 = -28.23 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,275,779 – 15,275,888
Length 109
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 83.28
Mean single sequence MFE -20.73
Consensus MFE -18.60
Energy contribution -17.83
Covariance contribution -0.77
Combinations/Pair 1.18
Mean z-score -0.82
Structure conservation index 0.90
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15275779 109 - 22224390
UCAAUUUGCUUCUAUAACACGCCUAAUCUGUGAUCCCCGCCCCACAAAAAAACAAAAACCCGGACACUACUGCUCCAUUUCCCAGCGGGCUGUUCCGCCUGAGGAGCAG
......(((((((......(((......((((..........))))...............(((((....)).)))........)))(((......)))..))))))). ( -21.50)
>DroSec_CAF1 99712 105 - 1
UCAAUUUGCUUCUAUAACACGCCUAAUCUGUGAUUCCCUCCC----AAAAAAAAAAAACCCGGACACUACUGCUCCAUUUCCCAGCGGGCUGUUCCGCCUGAGGAGCAG
......(((((((....((((.......))))..........----..............((((.((..(((((.........)))))...))))))....))))))). ( -20.90)
>DroYak_CAF1 87978 98 - 1
UCAAUUUGCUUCUAUAAUACGCCUAAUGCGUGAAUU--UGCC----A-----AAAAUACCCGAAUACUAUUGCUCCAUUUCCCAACGGGCUGUUUCGCCUAAGGAGCAG
......(((((((....(((((.....)))))....--.((.----.-----.(((((((((.......................)))).))))).))...))))))). ( -19.80)
>consensus
UCAAUUUGCUUCUAUAACACGCCUAAUCUGUGAUUCCCUCCC____AAAAAAAAAAAACCCGGACACUACUGCUCCAUUUCCCAGCGGGCUGUUCCGCCUGAGGAGCAG
......(((((((....((((.......))))............................((((.((..(((((.........)))))...))))))....))))))). (-18.60 = -17.83 +  -0.77)

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 11:59:41 2006