Locus 8006

Sequence ID X_DroMel_CAF1
Location 19,907,232 – 19,907,375
Length 143
Max. P 0.990168
window13142 window13143

overview

Window 2

Location 19,907,232 – 19,907,336
Length 104
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 76.45
Mean single sequence MFE -35.60
Consensus MFE -22.56
Energy contribution -22.92
Covariance contribution 0.36
Combinations/Pair 1.32
Mean z-score -2.37
Structure conservation index 0.63
SVM decision value 2.20
SVM RNA-class probability 0.990168
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19907232 104 + 22224390
GCCAAUUGUUGGCGCUUCGGUCGUGAAAGGGGGGCGUGGUGGGGGCGCGGCGAGGCCGGGUGAAAGGUGAAAGCCGAAAGGCGAAA---------GGUACGCCAGCAUGAAAC
(((..(..((.((((....).))).))..)..)))(((.(((.(((.((((...)))).))...........(((....)))....---------....).))).)))..... ( -38.80)
>DroSec_CAF1 21292 96 + 1
GCCAAUUGUUGGCGCUUCGGUCGUGAAAAG-GGGCGUGGUGAGGGCGUGGCGGGGCCGGGUGAAAGGUAAAAGCCGA-------AA---------GGUACGCCAGCAUGAAAC
((((.....))))(((.((.((.(....).-)).)).)))....((.(((((..(((........)))....(((..-------..---------))).)))))))....... ( -33.10)
>DroSim_CAF1 17372 96 + 1
GCCAAUUGUUGGCGCUUCGGUCGUGAAAGG-GGGCGUGGUGAGGGCGUGGCAGGGCCGGGUGAAAGGUAAAAGCCGA-------AA---------GGUACGCCAGCAUGAAAC
(((.....((.((((....).))).))...-.))).(.(((..(((((......(((........)))....(((..-------..---------))))))))..))).)... ( -33.10)
>DroEre_CAF1 20388 91 + 1
GCCAAUUGUUGGCGCUCCUGGCGGG--AA-----------GGGGGCGUGGCGGGGUCAGGUGAAAGGUGAAAGCCGAAAGCCGAAA---------GGUGCGCCAGCAUGAAAG
......(((((((((.(((..(((.--..-----------....((.((((...)))).))....(((....))).....)))..)---------)).)))))))))...... ( -38.10)
>DroYak_CAF1 21646 102 + 1
GCCAAUUGUUCGCGUUUUUGGGCGGAAAA-----------GAGGGCGUGGUGGGGCCAGGUGAAAGGUGAAAGCCGAAUGCCGAAAGGUACGAAAGGUACGCCAGCAUGAAAC
(((..((.(((((.(....).))))).))-----------...))).(((((..(((........(((....)))...((((....)))).....))).)))))......... ( -34.90)
>consensus
GCCAAUUGUUGGCGCUUCGGUCGUGAAAAG_GGGCGUGGUGAGGGCGUGGCGGGGCCGGGUGAAAGGUGAAAGCCGAA_G_CGAAA_________GGUACGCCAGCAUGAAAC
......((((((((..((..........................((.((((...)))).))....(((....)))....................))..))))))))...... (-22.56 = -22.92 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,907,268 – 19,907,375
Length 107
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 85.02
Mean single sequence MFE -37.66
Consensus MFE -28.88
Energy contribution -29.96
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -2.01
Structure conservation index 0.77
SVM decision value 0.85
SVM RNA-class probability 0.866586
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19907268 107 + 22224390
UGGUGGGGGCGCGGCGAGGCCGGGUGAAAGGUGAAAGCCGAAAGGCGAAA---------GGUACGCCAGCAUGAAACCGGGCAUUAGCCAACACUGCCAAUUGCAAUCAGCCCGAA
......((((..(((...(((.(((.....((....(((....)))....---------((....)).)).....))).)))....))).....(((.....)))....))))... ( -39.30)
>DroSec_CAF1 21327 100 + 1
UGGUGAGGGCGUGGCGGGGCCGGGUGAAAGGUAAAAGCCGA-------AA---------GGUACGCCAGCAUGAAACCGGGCAUUAGCCAACACUGCCAAUUGCAAUCAGCCCGAA
......((((.((((...(((.(((....(((....(((..-------..---------)))..)))........))).)))....))))....(((.....)))....))))... ( -35.20)
>DroSim_CAF1 17407 100 + 1
UGGUGAGGGCGUGGCAGGGCCGGGUGAAAGGUAAAAGCCGA-------AA---------GGUACGCCAGCAUGAAACCGGGCAUUAGCCAACACUGCCAAUUGCAAUCAGCCCGAA
.(((((..((.((((((...((((((...(((....(((..-------..---------)))..)))..)))....)))(((....)))....))))))...))..))).)).... ( -35.10)
>DroEre_CAF1 20415 102 + 1
----GGGGGCGUGGCGGGGUCAGGUGAAAGGUGAAAGCCGAAAGCCGAAA---------GGUGCGCCAGCAUGAAAGCGGGCAUUAGCCAACACUGCCAGUUGCAAUCAGCCC-AA
----..((((.((((((.((..(((....(((....)))(...(((....---------))).)(((.((......)).)))....))).)).))))))(.......).))))-.. ( -38.40)
>DroYak_CAF1 21675 112 + 1
----GAGGGCGUGGUGGGGCCAGGUGAAAGGUGAAAGCCGAAUGCCGAAAGGUACGAAAGGUACGCCAGCAUGAAACCGGGCAUUAGCCUACACUGCCAAUUGCAAUCAGCCCGAA
----..(((((((...((((..((((...(((....)))...((((....))))(....)...)))).((.((....)).))....)))).)))(((.....)))....))))... ( -40.30)
>consensus
UGGUGAGGGCGUGGCGGGGCCGGGUGAAAGGUGAAAGCCGAA_G_CGAAA_________GGUACGCCAGCAUGAAACCGGGCAUUAGCCAACACUGCCAAUUGCAAUCAGCCCGAA
......((((..(((...(((.(((....(((....)))....................((....))........))).)))....))).....(((.....)))....))))... (-28.88 = -29.96 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:06 2006