Locus 2084

Sequence ID 3R_DroMel_CAF1
Location 5,935,646 – 5,935,737
Length 91
Max. P 0.677848
window3405 window3406

overview

Window 5

Location 5,935,646 – 5,935,737
Length 91
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 81.00
Mean single sequence MFE -26.18
Consensus MFE -16.86
Energy contribution -16.83
Covariance contribution -0.03
Combinations/Pair 1.15
Mean z-score -1.74
Structure conservation index 0.64
SVM decision value 0.30
SVM RNA-class probability 0.677848
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5935646 91 + 27905053
UCGGCUGCGCUGCGUUCUCUUCGUUUUGCUUUUGCACAC--UUUCGCAGCUCGGCAACGUUCUACUGGAGUUGCCACCCGUUUACAAUCGGCG
..(((((((..(((.......)))..(((....)))...--...))))))).((((((.(((....)))))))))..(((........))).. ( -27.40)
>DroVir_CAF1 99825 89 + 1
UCGGCUGCGCUACGUUCUCUUCGCUUUGCUUUUGGACACUGCUUCGCAGCUCAGCA---UUCGGCA-AUGCUGCCAACUCGAUGCAAUUGUCU
..(((.(((............)))...)))...(((((.(((.(((.((..(((((---((....)-))))))....))))).)))..))))) ( -21.60)
>DroGri_CAF1 60796 90 + 1
UCGGCUGCGCUGCGUUCUCUUCGCUUUGCUUUUGCACACUGUUUCGCAGCUCAGCA---UUUAGCACGCGCUGCCAACUCGUUGCACUUACCU
..(((.((((.(((.......)))..((((..(((...(((.....)))....)))---...)))).)))).))).................. ( -26.10)
>DroEre_CAF1 39415 91 + 1
UCGGCUGCGCUGCGUUCUCUUCGUUUUGCUUUUGCACAC--UUUCGCAGCUCGGCAACGUUCUACUGGAGUUGCCACCCGUAAGCAAUCGGCG
(((..(((((((((........((..(((....))).))--...))))))..((((((.(((....)))))))))........)))..))).. ( -29.80)
>DroYak_CAF1 40841 91 + 1
UCGGCUGCGCUGCGUUCUCUUCGUUUUGCUUUUGCACAC--UUUCGCAGCUCGGCAACGUUCUACUGGAGUUGCCACCCGUAUGCAAUCGGCU
(((..(((((((((........((..(((....))).))--...))))))..((((((.(((....)))))))))........)))..))).. ( -29.60)
>DroMoj_CAF1 62637 89 + 1
UCGGCUGCGCUGCGUUCUCUUCGCUUUGCUUUUGCACACUACUUCGUAGCUCAGCA---UUCGACA-AUGCUGCCAACUUGAUGCAACCUCCU
..((.(((((((((............(((....)))........)))))).(((((---((....)-))))))..........))).)).... ( -22.55)
>consensus
UCGGCUGCGCUGCGUUCUCUUCGCUUUGCUUUUGCACAC__UUUCGCAGCUCAGCA___UUCUACAGGAGCUGCCAACCGGAUGCAAUCGGCU
...((((.((((((............(((....)))........)))))).))))...................................... (-16.86 = -16.83 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,935,646 – 5,935,737
Length 91
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 81.00
Mean single sequence MFE -26.88
Consensus MFE -16.58
Energy contribution -16.25
Covariance contribution -0.33
Combinations/Pair 1.30
Mean z-score -1.55
Structure conservation index 0.62
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5935646 91 - 27905053
CGCCGAUUGUAAACGGGUGGCAACUCCAGUAGAACGUUGCCGAGCUGCGAAA--GUGUGCAAAAGCAAAACGAAGAGAACGCAGCGCAGCCGA
..(((........)))..((((((...........))))))(.((((((...--((((((....))....(.....).))))..))))))).. ( -26.00)
>DroVir_CAF1 99825 89 - 1
AGACAAUUGCAUCGAGUUGGCAGCAU-UGCCGAA---UGCUGAGCUGCGAAGCAGUGUCCAAAAGCAAAGCGAAGAGAACGUAGCGCAGCCGA
.((((.((((.((((((...((((((-(....))---))))).))).))).)))))))).....((...(((.......)))...))...... ( -25.50)
>DroGri_CAF1 60796 90 - 1
AGGUAAGUGCAACGAGUUGGCAGCGCGUGCUAAA---UGCUGAGCUGCGAAACAGUGUGCAAAAGCAAAGCGAAGAGAACGCAGCGCAGCCGA
................(((((.((((.((((...---(((...((((.....))))..)))..))))..(((.......))).)))).))))) ( -28.30)
>DroEre_CAF1 39415 91 - 1
CGCCGAUUGCUUACGGGUGGCAACUCCAGUAGAACGUUGCCGAGCUGCGAAA--GUGUGCAAAAGCAAAACGAAGAGAACGCAGCGCAGCCGA
...((..(((.......(((((((...........))))))).((((((...--...(((....)))...(.....)..)))))))))..)). ( -26.80)
>DroYak_CAF1 40841 91 - 1
AGCCGAUUGCAUACGGGUGGCAACUCCAGUAGAACGUUGCCGAGCUGCGAAA--GUGUGCAAAAGCAAAACGAAGAGAACGCAGCGCAGCCGA
...((..(((.......(((((((...........))))))).((((((...--...(((....)))...(.....)..)))))))))..)). ( -27.30)
>DroMoj_CAF1 62637 89 - 1
AGGAGGUUGCAUCAAGUUGGCAGCAU-UGUCGAA---UGCUGAGCUACGAAGUAGUGUGCAAAAGCAAAGCGAAGAGAACGCAGCGCAGCCGA
....((((((..........((((((-(....))---))))).(((...........(((....)))..(((.......)))))))))))).. ( -27.40)
>consensus
AGCCGAUUGCAUACAGGUGGCAACUCCAGUAGAA___UGCCGAGCUGCGAAA__GUGUGCAAAAGCAAAACGAAGAGAACGCAGCGCAGCCGA
...((.((((........((((((....)).......))))..((((((.....((.(((....)))..))........)))))))))).)). (-16.58 = -16.25 +  -0.33)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:57 2006