Locus 3475

Sequence ID 2R_DroMel_CAF1
Location 11,672,772 – 11,672,904
Length 132
Max. P 0.866816
window5670 window5671

overview

Window 0

Location 11,672,772 – 11,672,892
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.21
Mean single sequence MFE -33.88
Consensus MFE -8.65
Energy contribution -10.05
Covariance contribution 1.40
Combinations/Pair 1.32
Mean z-score -1.90
Structure conservation index 0.26
SVM decision value 0.85
SVM RNA-class probability 0.866816
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11672772 120 - 20766785
UAUUUGAAGGACAUGAAGCUGGCUGCUGCUUUUCGCAAGCAACAGAAAAAGUCGCAGCUACAAGUUAGUCGCCGAAAAUUAGGAUUAGCUAAGCAGCGUCAACUAGGACGAUCCAAAAAG
........((((.....(((((((((.(((((((....).......)))))).)))))....((((((((............))))))))...))))(((......)))).)))...... ( -31.61)
>DroSec_CAF1 12832 120 - 1
UAUUUUGAGGACAUGGAAAUGGCUGCUGGUUUACGGAAGCACAAGAAAAAGUCGCAGCAACACGGUUAUCACCGAAAAUUAGGAUUAGCUAAGCAGCGUCAACCAGGACGAAUCAAAAAG
..((((((((.(((....))).)).((((((.(((...((((........)).)).((....((((....))))....((((......))))))..))).))))))......)))))).. ( -27.60)
>DroSim_CAF1 8806 120 - 1
UAUUUUGAGGACAUGGAAAUGGCUGCUUGUUUGCCGAAGCAAAAGAAAAAGUCGCAGCAACACGGUUAUCGCCGAAAAUUAGGAUUAGCUAAGCUGCGUCAACCAGGACGAAUCAAAAAG
..(((((((..(.(((....((((.....(((((....)))))......))))(((((....((((....))))....((((......))))))))).....))))..)...)))))).. ( -31.10)
>DroEre_CAF1 8642 108 - 1
UACUUGGAGAACAUGGAGCUGGGUGUUGCUUUUCGGAAGCAACAGCAAAAGCAGCAGCUCCAAAGUAGUCGCCGAAGAUUAGGUGGAGCUGGACCACGUCGAC------------UAGGA
..(((((.((...(((.(((.(.(((((((((...))))))))).)...)))..((((((((...(((((......)))))..))))))))..)))..))..)------------)))). ( -43.30)
>DroYak_CAF1 8835 111 - 1
UACUUGGAGGACAUGGAGCUGGGUGCUACUUUUCGGAAGCAACAGCAAAAGCAGCAGCUUCUAAGUAGUCGCCGUAGUUUGGGUGUAGCUGGACCAAGACGAU---------CCCCAAAG
...((((.((((...((((((((((((((((...((((((..(.((....)).)..)))))))))))).)))).)))))).(((.(....).))).....).)---------)))))).. ( -35.80)
>consensus
UAUUUGGAGGACAUGGAGCUGGCUGCUGCUUUUCGGAAGCAACAGAAAAAGUCGCAGCUACAAGGUAGUCGCCGAAAAUUAGGAUUAGCUAAGCAGCGUCAAC_AGGACGA_CCAAAAAG
.........(((.(((.....(((((.(((((((....).......)))))).)))))....................((((......)))).))).))).................... ( -8.65 = -10.05 +   1.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,672,812 – 11,672,904
Length 92
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 66.48
Mean single sequence MFE -24.84
Consensus MFE -7.88
Energy contribution -10.12
Covariance contribution 2.24
Combinations/Pair 1.30
Mean z-score -1.88
Structure conservation index 0.32
SVM decision value 0.00
SVM RNA-class probability 0.534980
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11672812 92 + 20766785
AAUUUUCGGCGACUAACUUGUAGCUGCGACUUUUUCUGUUGCUUGCGAAAAGCAGCAGCCAGCUUCAUGUCCUUCAAAUAAUCGUCGACCUU----------------------------
.....(((((((.((((.((.(((((.(.......(((((((((.....))))))))))))))).)).))........)).)))))))....---------------------------- ( -26.01)
>DroSec_CAF1 12872 92 + 1
AAUUUUCGGUGAUAACCGUGUUGCUGCGACUUUUUCUUGUGCUUCCGUAAACCAGCAGCCAUUUCCAUGUCCUCAAAAUAUUUGCUGACCUU----------------------------
......((((....)))).(((((((.(((........))((....))...)))))))).........(((..(((.....)))..)))...---------------------------- ( -14.30)
>DroSim_CAF1 8846 92 + 1
AAUUUUCGGCGAUAACCGUGUUGCUGCGACUUUUUCUUUUGCUUCGGCAAACAAGCAGCCAUUUCCAUGUCCUCAAAAUAUUUGCUAACCUU----------------------------
.(((((.((.((((.....((.(((((((.....)).(((((....)))))...))))).)).....)))))).))))).............---------------------------- ( -19.60)
>DroEre_CAF1 8670 120 + 1
AAUCUUCGGCGACUACUUUGGAGCUGCUGCUUUUGCUGUUGCUUCCGAAAAGCAACACCCAGCUCCAUGUUCUCCAAGUAAUCGCUGACCUUGGAUGCCGAUUCGGGGCCUACUGUACUC
.....(((((((.(((((((((((((..((....))((((((((.....))))))))..))))))))........))))).)))))))((((((((....))))))))............ ( -43.60)
>DroYak_CAF1 8866 93 + 1
AAACUACGGCGACUACUUAGAAGCUGCUGCUUUUGCUGUUGCUUCCGAAAAGUAGCACCCAGCUCCAUGUCCUCCAAGUAAUC---------------------------CACUUUACUC
.......((.(.((((((.(((((.((.((....)).)).)))))....))))))).)).................(((((..---------------------------....))))). ( -20.70)
>consensus
AAUUUUCGGCGACUACCUUGUAGCUGCGACUUUUUCUGUUGCUUCCGAAAAGCAGCAGCCAGCUCCAUGUCCUCCAAAUAAUCGCUGACCUU____________________________
.....(((((((..........((((..(((....(((((((((.....)))))))))..)))..)).))...........)))))))................................ ( -7.88 = -10.12 +   2.24)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:29 2006