Locus 2202

Sequence ID 2R_DroMel_CAF1
Location 8,128,234 – 8,128,392
Length 158
Max. P 0.998048
window3632 window3633

overview

Window 2

Location 8,128,234 – 8,128,352
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 65.77
Mean single sequence MFE -28.32
Consensus MFE -14.39
Energy contribution -14.47
Covariance contribution 0.08
Combinations/Pair 1.61
Mean z-score -1.81
Structure conservation index 0.51
SVM decision value 0.97
SVM RNA-class probability 0.891815
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8128234 118 - 20766785
GCAACGCCUUACAUCCUUCA-AAUAAGGAUGGCAACGCCAGACAUCCUUAAAAAUAAGGAUGGCAGUGCGCCAUAUUCUCAUAAUUCAGGAUGGCAAUGCCUGAUAGCUUUAGGAAA-GA
(((..(((...(((((((..-...)))))))............(((((((....))))))))))..)))((((..((((........))))))))....(((((.....)))))...-.. ( -34.70)
>DroSec_CAF1 14542 117 - 1
GCAACGCCUGACGUCCUUAAAAAUAAGGAUGGCAACGCCGUAUAUCCUUAGAAAAAAGGAUGGCAGCGCGCAGUAUUCUCAAAAUUAAGGAUGGCAAUGCC-GAUAGCCUUAG-AAU-UA
((..((((((.(((((((.....((((((((((...)))....))))))).....))))))).))).)))..))..........((((((.((((...)))-)....))))))-...-.. ( -35.70)
>DroSim_CAF1 5402 116 - 1
GCAACGCCUGACGUCCUUAAAAAUAAGGAUGGCAACGCCGUAUAUCCUUAGAAA-AAGGAUGGCAGCGCGCAGUAUUCUCUAAAUUUAGGAUGGCAAUGCC-GAUAGCCUUAG-AAU-UA
((..((((((.(((((((.....((((((((((...)))....)))))))....-))))))).))).)))..))....(((((..(((...((((...)))-).)))..))))-)..-.. ( -33.10)
>DroEre_CAF1 5471 92 - 1
------------------------UGGGGUGGCAGCACCGGAUAUUAUAAACAUAUAUGGUGGCAGCGCCCGAUAUCCU---AAAUCCGGAUGACAGCGACCUACAGCUUUAA-AAAAUA
------------------------..((((.((..((((((((.(((.....((((..((((....))))..))))..)---)))))))).))...)).))))..........-...... ( -23.10)
>DroYak_CAF1 14897 116 - 1
GCAACACCCGGCAUUCUUAACAAAUAAAGUGGUAGCGUCCGAAAUCCUUAGAAAUCAGGAUGGCAUUAUAAAACAUUCUCAAAAAUCAUAAUGGCAACACCCGACAGCUUUAA-AAA---
((........))............((((((.((.......(..(((((.(....).)))))..)...........................((....))....)).)))))).-...--- ( -15.00)
>consensus
GCAACGCCUGACAUCCUUAA_AAUAAGGAUGGCAACGCCGGAUAUCCUUAGAAAAAAGGAUGGCAGCGCGCAAUAUUCUCAAAAUUCAGGAUGGCAAUGCC_GAUAGCUUUAG_AAA_UA
...........((((((........((((((....((((...(((((((......)))))))...).)))...))))))........))))))........................... (-14.39 = -14.47 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,128,273 – 8,128,392
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.61
Mean single sequence MFE -33.30
Consensus MFE -26.31
Energy contribution -25.25
Covariance contribution -1.06
Combinations/Pair 1.47
Mean z-score -2.67
Structure conservation index 0.79
SVM decision value 2.99
SVM RNA-class probability 0.998048
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8128273 119 - 20766785
UAUUCAUGUGUGUCAAUACACAUUCUUAGCAAUAAGGUUGGCAACGCCUUACAUCCUUCA-AAUAAGGAUGGCAACGCCAGACAUCCUUAAAAAUAAGGAUGGCAGUGCGCCAUAUUCUC
.....(((((((....)))))))(((((....))))).((((.........(((((((..-...)))))))(((..((((....((((((....))))))))))..)))))))....... ( -38.00)
>DroSec_CAF1 14579 120 - 1
UACACAUGUGUGUCAAUACACAUUCUUAGCAUUUAGGACGGCAACGCCUGACGUCCUUAAAAAUAAGGAUGGCAACGCCGUAUAUCCUUAGAAAAAAGGAUGGCAGCGCGCAGUAUUCUC
(((..(((((((....))))))).....((..(((((.((....)))))))((((((((....))))))))))...(((((.(((((((......)))))))...))).)).)))..... ( -39.40)
>DroSim_CAF1 5439 119 - 1
UACACAUGUGUGUCAAAACACAUUCUUGGCAUUUACGACGGCAACGCCUGACGUCCUUAAAAAUAAGGAUGGCAACGCCGUAUAUCCUUAGAAA-AAGGAUGGCAGCGCGCAGUAUUCUC
(((.((.((((((....))))))...))((.........(....)(((((.(((((((.....((((((((((...)))....)))))))....-))))))).))).)))).)))..... ( -35.50)
>DroYak_CAF1 14933 118 - 1
UACACAUGUGUAUCAAUACAAA--CUUAGGAAUUGUGAUGGCAACACCCGGCAUUCUUAACAAAUAAAGUGGUAGCGUCCGAAAUCCUUAGAAAUCAGGAUGGCAUUAUAAAACAUUCUC
......(((((....)))))..--....((((((((((((.(......(((.((.((..((.......))...)).)))))..(((((.(....).)))))).)))))))....))))). ( -20.30)
>consensus
UACACAUGUGUGUCAAUACACAUUCUUAGCAAUUAGGACGGCAACGCCUGACAUCCUUAAAAAUAAGGAUGGCAACGCCGGAUAUCCUUAGAAAUAAGGAUGGCAGCGCGCAAUAUUCUC
......((((((................((..(((((.((....)))))))(((((((......)))))))))...(((....(((((((....))))))))))..))))))........ (-26.31 = -25.25 +  -1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:45 2006