Locus 8668

Sequence ID X_DroMel_CAF1
Location 21,954,572 – 21,954,691
Length 119
Max. P 0.790993
window14251 window14252

overview

Window 1

Location 21,954,572 – 21,954,666
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.96
Mean single sequence MFE -30.98
Consensus MFE -19.88
Energy contribution -19.75
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -1.81
Structure conservation index 0.64
SVM decision value 0.56
SVM RNA-class probability 0.781367
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21954572 94 + 22224390
--------------------UGCAAUUGCCA-AAUUGCAUAUGCAAUUAAAUUGGGAAGAGCCAAAUGAGC-----CAGUUGGCGGAGCAACAAGGAUACCUGGCCAGGUGUGCGAGAAA
--------------------(((((((....-)))))))..(((.......((((......))))....((-----(....)))...)))....(.((((((....)))))).)...... ( -26.00)
>DroSec_CAF1 12917 119 + 1
CCAGGACUGCAACCAAAAAAAGAACUUGCCA-AAUUGCAUAUGCAAUCAAAUUGGGAAGAGCCAAAUGAGCCUUGCCACUUGGCGGUGUAAAAAGGAAGCCCGCCCAGGUGCGCGAGAAA
...((.......))..........(((.(((-((((((....)))))....)))).))).(((....).))(((((((((((((((.((.........))))).))))))).)))))... ( -34.40)
>DroSim_CAF1 4611 119 + 1
CCAGGACUGCAACCAAAAAAAGAACUUGCCA-AAUUGCAUAUGCAAUCAAAUUGGGAAGAGCCAAAUGAGCCUUGCCACUUGGCGGUGCAAAAAGGAAGCCUGGCCAGGUGCGCGAGAAA
...((.......))..........(((.(((-((((((....)))))....)))).))).(((....).))(((((((((((((.(.((.........)).).)))))))).)))))... ( -34.80)
>DroYak_CAF1 11279 116 + 1
CCAGGAGUUUAACCGAAAA----AAUUGCCAAAAUUGCAAAUGCUAUCAGACUGCGAAGAGCCAAAUGAGCCUUGCCAGUUGGCGGUGCAAAAAAGGAGCCCGUGCAGGUGCGCAAGAAA
...((.......)).....----..((((((...(((((...(((.......((((....(((((.((.((...)))).)))))..)))).......)))...))))).)).)))).... ( -28.74)
>consensus
CCAGGACUGCAACCAAAAA_AGAAAUUGCCA_AAUUGCAUAUGCAAUCAAAUUGGGAAGAGCCAAAUGAGCCUUGCCACUUGGCGGUGCAAAAAGGAAGCCCGGCCAGGUGCGCGAGAAA
........................(((((((..(((((....)))))....((((.....(((((.((........)).)))))((.((.........))))..)))).)).)))))... (-19.88 = -19.75 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,954,591 – 21,954,691
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.68
Mean single sequence MFE -32.15
Consensus MFE -16.32
Energy contribution -16.40
Covariance contribution 0.08
Combinations/Pair 1.20
Mean z-score -1.91
Structure conservation index 0.51
SVM decision value 0.59
SVM RNA-class probability 0.790993
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21954591 100 + 22224390
AUGCAAUUAAAUUGGGAAGAGCCAAAUGAGC-----CAGUUGGCGGAGCAACAAGGAUACCUGGCCAGGUGUGCGAGAAAAUUCGUG-----------G--GAGAGUGGCAGAAAAGG--
...........((((......))))....((-----((.((.(((((.......(.((((((....)))))).).......))))).-----------.--..)).))))........-- ( -24.64)
>DroSec_CAF1 12956 105 + 1
AUGCAAUCAAAUUGGGAAGAGCCAAAUGAGCCUUGCCACUUGGCGGUGUAAAAAGGAAGCCCGCCCAGGUGCGCGAGAAAAUUCGUG-----------G--GAGAGUGGCAGAAAAGC--
..((..(((..((((......)))).)))...((((((((((((((.((.........)))))))......((((((....))))))-----------.--..)))))))))....))-- ( -31.90)
>DroSim_CAF1 4650 105 + 1
AUGCAAUCAAAUUGGGAAGAGCCAAAUGAGCCUUGCCACUUGGCGGUGCAAAAAGGAAGCCUGGCCAGGUGCGCGAGAAAACUCGUG-----------G--GAGAGUGGCAGAAAAGC--
.(((..((...((((......))))(((((.(((((((((((((.(.((.........)).).)))))))).)))))....))))).-----------.--..))...))).......-- ( -34.30)
>DroEre_CAF1 4563 112 + 1
AUGCUAUCAAAUUUCGAAGGGCCAAAUGAGCCUUGCCAGUUGGCGGUGCAAAAAGGAAGCCCUGUGAGGUGCA--AGAGG----UGGCAGGAGAACCCGGAGGAAGUGGCAGAAAAGG--
.((((((....((((...(((.....((.((((((((....))).(..(....(((....))).....)..).--.))))----)..))......)))...)))))))))).......-- ( -30.90)
>DroYak_CAF1 11315 118 + 1
AUGCUAUCAGACUGCGAAGAGCCAAAUGAGCCUUGCCAGUUGGCGGUGCAAAAAAGGAGCCCGUGCAGGUGCGCAAGAAAAUUUGGGCAGAAGCGGCAG--GGAAGUGGCAGAAAAGGGU
.((((((....((((......((((((....(((((((.(((((((.((.........)))))).))).)).)))))...))))))((....)).))))--....))))))......... ( -39.00)
>consensus
AUGCAAUCAAAUUGGGAAGAGCCAAAUGAGCCUUGCCAGUUGGCGGUGCAAAAAGGAAGCCCGGCCAGGUGCGCGAGAAAAUUCGUG___________G__GAGAGUGGCAGAAAAGG__
....................((((.....((.(((((....))))).)).........((((.....)).))..................................)))).......... (-16.32 = -16.40 +   0.08)

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 13:09:54 2006