Locus 989

Sequence ID 2R_DroMel_CAF1
Location 4,146,788 – 4,146,901
Length 113
Max. P 0.938480
window1756 window1757

overview

Window 6

Location 4,146,788 – 4,146,878
Length 90
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 84.77
Mean single sequence MFE -19.00
Consensus MFE -14.23
Energy contribution -14.22
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.75
SVM decision value 0.71
SVM RNA-class probability 0.829221
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4146788 90 - 20766785
AACUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGCAACACGCAGCGAAAAUUUGCAUAAUAAUAAGUCUAUAU-----U------------
....(((....((((((((.....)))))))).................((.....)).((((....))))..........))).....-----.------------ ( -16.70)
>DroSec_CAF1 12217 90 - 1
AACUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGCAGCACGCAGCGAAAAUUUGCAUAAUAAUAAAUCUAUAU-----C------------
...(((.....((((((((.....)))))))))))..............((.....)).((((....))))..................-----.------------ ( -15.70)
>DroSim_CAF1 16515 90 - 1
AACUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGCAGCACGCAGCGAAAAUUUGCAUAAUAAUAAAACUAUAU-----C------------
...(((.....((((((((.....)))))))))))..............((.....)).((((....))))..................-----.------------ ( -15.70)
>DroEre_CAF1 11295 107 - 1
AACUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGGCACACGCAGAGAAAAUUUGCAUAGUAAUGAACCUGUGAGCUAUCUAUAUUAUUUUU
...((((....((((((((.....)))))))).............((((((.....(((((.....))))).((....))..)))))).)))).............. ( -27.90)
>consensus
AACUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGCAACACGCAGCGAAAAUUUGCAUAAUAAUAAAUCUAUAU_____C____________
...(((.....((((((((.....))))))))))).....................((((.......)))).................................... (-14.23 = -14.22 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,146,809 – 4,146,901
Length 92
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 73.33
Mean single sequence MFE -26.70
Consensus MFE -17.67
Energy contribution -17.84
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.66
SVM decision value 1.29
SVM RNA-class probability 0.938480
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4146809 92 - 20766785
CGGCUAUUAAGUCUUGGC-----CAGCCAAC-----------UGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGCAACACGCAGCGAAAAUUU
.(((((........))))-----).(((...-----------.)))....((((((((.....)))))))).................((.....))........... ( -24.00)
>DroPse_CAF1 5450 106 - 1
CGGCUAUUAAGUCGCGGACGAGCCAGCCAACCGAGGCACAGUUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUAUACCAGUACUCGUAGCAGCAGC--
.((((....))))((..(((((...((((((.(.....).))))))....((((((((.....)))))))).....................))))).))......-- ( -32.20)
>DroGri_CAF1 10845 98 - 1
CGGCUAUUAAGUCU-GGC-----CAGCCAACCAAGACACAGUUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACACACACACACAAGGAACAG--CA--CA
.(((((.......)-)))-----).((((((.........))))))....((((((((.....)))))))).............................--..--.. ( -25.30)
>DroEre_CAF1 11333 92 - 1
CGGCUAUUAAGUCUUGGC-----CAGCCAAC-----------UGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAGGCACACGCAGAGAAAAUUU
.(((((........))))-----).(((...-----------.(....).((((((((.....)))))))).................)))................. ( -24.40)
>DroAna_CAF1 13397 85 - 1
CGGCUAUUAAGUCUUGGCCAGGCCAGCCAGU-----------UGGCAACUUGGGUGGCAACAUGGCAUUCACCAAUCACACAUACUCGUAUACCCG------------
.(((((........)))))..(((((....)-----------)))).....(((((....).(((......))).................)))).------------ ( -23.30)
>DroPer_CAF1 8133 105 - 1
CGGCUAUUAAGUCGCGGCCGAGCCAGCCAACCGAGGCACAGUUGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUAUACCAGUUCUCGUAGCAGCAG---
.((((....))))((.((((((...((((((.(.....).))))))....((((((((.....)))))))).....................))))..)).))..--- ( -31.00)
>consensus
CGGCUAUUAAGUCUUGGC_____CAGCCAAC___________UGGCAACUUGGGUGGCAACAUGCCAUUCACCAAUCACACAUACACAAGUACACGCAGC__CA____
.((((....))))..((........((((.............))))....((((((((.....))))))))))................................... (-17.67 = -17.84 +   0.17)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:31 2006