Locus 5676

Sequence ID 2R_DroMel_CAF1
Location 18,010,645 – 18,010,741
Length 96
Max. P 0.920554
window9091 window9092

overview

Window 1

Location 18,010,645 – 18,010,741
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 86.47
Mean single sequence MFE -23.20
Consensus MFE -17.18
Energy contribution -18.18
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.74
SVM decision value 1.14
SVM RNA-class probability 0.920554
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18010645 96 + 20766785
UGCCAGCACCACCAACUGCCCGCACCACCCAACCGCAAGUGGUGCCCCGCCCACGCUGCCUGCCUAGCCCGCCCGCAGCCUUAUUGCAGCAUUAUU
(((..(((.........((..(((((((..........)))))))...))....(((((..((.......))..))))).....))).)))..... ( -25.30)
>DroSec_CAF1 24719 87 + 1
UGCAAGCACCGCCAACUGCCCGCACCACCCAACCGCAAGUGGUGCCCCGCCCACGCUGCCUGCCUAUCCCGCCCGCAGCC---------CAUUAUU
.((..(((........)))..(((((((..........)))))))...))....(((((..((.......))..))))).---------....... ( -22.60)
>DroSim_CAF1 23688 87 + 1
UGCAAGCACCGCCAACUGCCCGCACCACCCAACCGCAAGUGGCGCCCCGCCCACGCUGCCUGCCUAUCCCGCCCGCAGCC---------CAUUAUU
(((..(((........)))..)))..............((((.((...))))))(((((..((.......))..))))).---------....... ( -19.80)
>DroEre_CAF1 26094 83 + 1
UGCUAGCACCACCAACUGCACGCACCACUCAACCGCAAGUGGUGCCCCACCCAUGCUGC----CGCUCCCGCCCGCAGCC---------CAUUAUU
.....(((........)))..((((((((........)))))))).........(((((----.((....))..))))).---------....... ( -23.60)
>DroYak_CAF1 23626 83 + 1
UGCCAGCACCACCAACUGCACGCACCACUCAACCGCAAGUGGUGCCCCACCCAGGCUGC----CUUUUCCGCCCGCAGCC---------CAUUAUU
.....(((........)))..((((((((........))))))))........((((((----...........))))))---------....... ( -24.70)
>consensus
UGCAAGCACCACCAACUGCCCGCACCACCCAACCGCAAGUGGUGCCCCGCCCACGCUGCCUGCCUAUCCCGCCCGCAGCC_________CAUUAUU
.....(((........)))..(((((((..........))))))).........(((((..((.......))..)))))................. (-17.18 = -18.18 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,010,645 – 18,010,741
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 86.47
Mean single sequence MFE -35.78
Consensus MFE -27.38
Energy contribution -27.62
Covariance contribution 0.24
Combinations/Pair 1.21
Mean z-score -2.12
Structure conservation index 0.77
SVM decision value 1.03
SVM RNA-class probability 0.903316
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18010645 96 - 20766785
AAUAAUGCUGCAAUAAGGCUGCGGGCGGGCUAGGCAGGCAGCGUGGGCGGGGCACCACUUGCGGUUGGGUGGUGCGGGCAGUUGGUGGUGCUGGCA
.....(((((((....((((((...(.(.(((.((.....)).))).).).(((((((((......)))))))))..)))))).....))).)))) ( -39.40)
>DroSec_CAF1 24719 87 - 1
AAUAAUG---------GGCUGCGGGCGGGAUAGGCAGGCAGCGUGGGCGGGGCACCACUUGCGGUUGGGUGGUGCGGGCAGUUGGCGGUGCUUGCA
.......---------..(((....))).....(((((((.(((.(((...(((((((((......))))))))).....))).))).))))))). ( -37.50)
>DroSim_CAF1 23688 87 - 1
AAUAAUG---------GGCUGCGGGCGGGAUAGGCAGGCAGCGUGGGCGGGGCGCCACUUGCGGUUGGGUGGUGCGGGCAGUUGGCGGUGCUUGCA
.......---------..(((....))).....(((((((.(((.(((...(((((((((......))))))))).....))).))).))))))). ( -37.10)
>DroEre_CAF1 26094 83 - 1
AAUAAUG---------GGCUGCGGGCGGGAGCG----GCAGCAUGGGUGGGGCACCACUUGCGGUUGAGUGGUGCGUGCAGUUGGUGGUGCUAGCA
.......---------.(((....((....))(----(((.(((.((((.((((((((((......))))))))).).)).)).))).))))))). ( -32.70)
>DroYak_CAF1 23626 83 - 1
AAUAAUG---------GGCUGCGGGCGGAAAAG----GCAGCCUGGGUGGGGCACCACUUGCGGUUGAGUGGUGCGUGCAGUUGGUGGUGCUGGCA
......(---------((((((...........----)))))))...((.((((((((((......))))))))).).))((..(.....)..)). ( -32.20)
>consensus
AAUAAUG_________GGCUGCGGGCGGGAUAGGCAGGCAGCGUGGGCGGGGCACCACUUGCGGUUGGGUGGUGCGGGCAGUUGGUGGUGCUGGCA
.................(((((..((.......))..)))))....((...(((((((((......)))))))))..)).((((((...)))))). (-27.38 = -27.62 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:34 2006