Locus 2827

Sequence ID 2R_DroMel_CAF1
Location 9,826,194 – 9,826,331
Length 137
Max. P 0.939770
window4673 window4674

overview

Window 3

Location 9,826,194 – 9,826,304
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.81
Mean single sequence MFE -31.97
Consensus MFE -18.96
Energy contribution -19.10
Covariance contribution 0.14
Combinations/Pair 1.31
Mean z-score -3.02
Structure conservation index 0.59
SVM decision value 1.28
SVM RNA-class probability 0.939770
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9826194 110 - 20766785
GUAUCUGUUGUAUGGAUAUGGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUUAGCGAAUUCCUCGCACUCUUUGCAAUGCCAGUACUAAUUU
((((((((..((....))..))))))))..........((((---------...((((((.(((-((........))))).((((.....))))..........))))))))))...... ( -32.40)
>DroSec_CAF1 63900 104 - 1
GUAUCUGUUGUAUGAAUAUGGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUUAGCGAAUUCC------UCUUUGCAAUGCCAGUACUAAUUU
((((((((..((....))..))))))))..........((((---------...((((((.(((-((........))))).(((((....------..))))).))))))))))...... ( -31.20)
>DroSim_CAF1 65426 104 - 1
GUAUCUGUUGUAUGAAUAUGGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUUAGCGAAUUCC------UCUUUGCAAUGCCAGUACUAAUUU
((((((((..((....))..))))))))..........((((---------...((((((.(((-((........))))).(((((....------..))))).))))))))))...... ( -31.20)
>DroEre_CAF1 68728 110 - 1
GUAUCUGGUCUAUGGAUACAGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUUAGCGAAUUCCUCGCACUCUAUGCAAUGCCUGUACGAAUUU
((((((((((....)))....))))))).........(((((---------(.((.((((((((-((........)))...((((.....))))..)))))))...)).))))))..... ( -32.10)
>DroYak_CAF1 65894 110 - 1
GUAUCUGCUGUAUGGAUACAGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUUAGCGAAUUCCUCGCACUCUAUGCAAUGGCUGUACACAUUU
((((((((((((....))))))))))))..........((((---------(.((.((((((((-((........)))...((((.....))))..)))))))....)))))))...... ( -38.80)
>DroAna_CAF1 63898 119 - 1
GUAUCUUCCACCUGGGAGCGACAGAUACGGAUACAGAUACAGAUGGCGGCGGAGUAGUAUGGGGACACAAAUAUUUGUUUAGCGAAUUCCUAGCACUUUGUGGAAGUUAAAUACGAAA-U
(((((((((((((((((((((((((((((....((........))....))........((....))....))))))))..))....))))))......)))))))....))))....-. ( -26.10)
>consensus
GUAUCUGUUGUAUGGAUACGGCAGAUACAAAUACACACGUAC_________AAGUGGUAUGGAG_CACAAAUAUUUGCUUAGCGAAUUCCUCGCACUCUUUGCAAUGCCAGUACUAAUUU
((((((((((((....))))))))))))..((((.(((...............)))))))((((........((((((...))))))........))))..................... (-18.96 = -19.10 +   0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,826,234 – 9,826,331
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.64
Mean single sequence MFE -29.07
Consensus MFE -17.39
Energy contribution -17.48
Covariance contribution 0.09
Combinations/Pair 1.29
Mean z-score -2.09
Structure conservation index 0.60
SVM decision value 0.51
SVM RNA-class probability 0.764807
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9826234 97 - 20766785
-----CAA--UAAGAU---G---CUGGCCCAAGGUGGAAAGUAUCUGUUGUAUGGAUAUGGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUU
-----...--..((((---(---.((((((..........((((((((..((....))..))))))))..((((.(((....---------..))))))))).)-).))..))))).... ( -25.40)
>DroSec_CAF1 63934 100 - 1
-----CAA--UGAGAU---GCUGCUGGCCCAAGGUGGAAAGUAUCUGUUGUAUGAAUAUGGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUU
-----...--....((---((..((........(((....((((((((..((....))..)))))))).....)))......---------.))..)))).(((-((........))))) ( -27.86)
>DroSim_CAF1 65460 100 - 1
-----CAA--UGAGAU---GCUGCUGGCCCAAGGUGGAAAGUAUCUGUUGUAUGAAUAUGGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUU
-----...--....((---((..((........(((....((((((((..((....))..)))))))).....)))......---------.))..)))).(((-((........))))) ( -27.86)
>DroEre_CAF1 68768 97 - 1
-----CAG--UGAGAU---G---CUGGCCCAAGGUGGAAAGUAUCUGGUCUAUGGAUACAGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUU
-----..(--((((((---(---((..((......))..))))))).((((.((....))..)))).......))).(((((---------.....)))))(((-((........))))) ( -24.60)
>DroYak_CAF1 65934 97 - 1
-----CAG--UGAGAU---G---CUGGCCCAAGGUGGAAAGUAUCUGCUGUAUGGAUACAGCAGAUACAAAUACACACGUAC---------AAGUGGUAUGGAG-CACAAAUAUUUGCUU
-----(((--(.....---)---)))((((..........((((((((((((....))))))))))))..((((.(((....---------..))))))))).)-).............. ( -32.70)
>DroAna_CAF1 63937 120 - 1
CUUAUCAUUCCGCGAUGCUGCUGCUGCUCCAAGGUAGAAAGUAUCUUCCACCUGGGAGCGACAGAUACGGAUACAGAUACAGAUGGCGGCGGAGUAGUAUGGGGACACAAAUAUUUGUUU
..(((.(((((((..((((.(((.((((((.((((.(((......))).)))).)))))).)))....(....)..........))))))))))).)))((....))............. ( -36.00)
>consensus
_____CAA__UGAGAU___G___CUGGCCCAAGGUGGAAAGUAUCUGUUGUAUGGAUACGGCAGAUACAAAUACACACGUAC_________AAGUGGUAUGGAG_CACAAAUAUUUGCUU
...............................(((..((..((((((((((((....))))))))))))..((((.(((...............))))))).............))..))) (-17.39 = -17.48 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:27 2006