Locus 4716

Sequence ID 2L_DroMel_CAF1
Location 13,534,291 – 13,534,462
Length 171
Max. P 0.817806
window7463 window7464

overview

Window 3

Location 13,534,291 – 13,534,387
Length 96
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 78.48
Mean single sequence MFE -27.80
Consensus MFE -14.87
Energy contribution -15.10
Covariance contribution 0.23
Combinations/Pair 1.21
Mean z-score -2.52
Structure conservation index 0.53
SVM decision value 0.48
SVM RNA-class probability 0.753083
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13534291 96 - 22407834
UUCAAAACGAAGGUAGUGCAAUACAUUCAUACAUACAUAUGUAUGUACAA---------UAUAUACCGAAAGG--CAAAGGAGCCACGGCGGGUACCCUCUGCUGAG
(((.....(((.(((......))).))).(((((((....)))))))...---------........))).((--(......))).(((((((.....))))))).. ( -24.00)
>DroSim_CAF1 17056 95 - 1
UUCAAAACGAAGGUAGUGCA-----UACAAACAUACA----UAUGUACAA-UAUGUAUGUAUAUACCGAAAGG--CAAAGGAGCCACGGUGGGUCCCCUCUGCUGAG
...........((((((((.-----.....(((((((----(((.....)-)))))))))......(....))--))..(((.((.....)).)))...)))))... ( -26.60)
>DroEre_CAF1 20494 105 - 1
UACAAAACGAAGGUACUGCA-UACAUACAUAUGUAUGUAUGUAUGUACGAGUAUGUAC-AAUAUAACGAAAGGAGCAAAGGAGCCACGGUGGGUGCCCUCUGCUGAG
((((..((....((((((((-(((((((....))))))))))).))))..)).)))).-.......(....).((((.(((.(((......)))..))).))))... ( -32.80)
>consensus
UUCAAAACGAAGGUAGUGCA_UACAUACAUACAUACAUAUGUAUGUACAA_UAUGUA__UAUAUACCGAAAGG__CAAAGGAGCCACGGUGGGUACCCUCUGCUGAG
...........(((...............(((((((....)))))))..................((....)).........))).(((((((.....))))))).. (-14.87 = -15.10 +   0.23)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,534,348 – 13,534,462
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 91.78
Mean single sequence MFE -32.73
Consensus MFE -27.68
Energy contribution -27.93
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.85
SVM decision value 0.67
SVM RNA-class probability 0.817806
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13534348 114 - 22407834
GCCAACGGGUUAAGGAUGUCCUGGCCUGGGGAAAACUGAAAGAUAUGUGGGCAUAGUCAGUGGGUAGCAGGGCGUUUCAAAACGAAGGUAGUGCAAUACAUUCAUACAUACAUA
(((..(((((((.((....)))))))))......(((((....((((....)))).))))).))).(((..((.((((.....))))))..))).................... ( -28.70)
>DroSim_CAF1 17119 107 - 1
GCCAACGGGUUAAGGAUGUCCUGGCCUGGGGAAAACUGAAAGAUAUGUGGGCAUAGUCAGUGGGUAGCAGGGCGUUUCAAAACGAAGGUAGUGCA-----UACAAACAUACA--
.((..(((((((.((....)))))))))......(((((....((((....)))).)))))))((((((..((.((((.....))))))..))).-----))).........-- ( -29.10)
>DroEre_CAF1 20561 113 - 1
GCCAACGGGUUAAGGAUGUCCUGGCCUGGGGAAACCUGAAAGAUAUGUGGGCAUAGUCAGUGGGUAGCAGGGCGUUACAAAACGAAGGUACUGCA-UACAUACAUAUGUAUGUA
(((..((..((...((((((((((((((((....)))....((((((....))).)))...))))..)))))))))..))..))..)))..((((-(((((....))))))))) ( -39.50)
>DroYak_CAF1 21068 113 - 1
GCCAACGGGUUAAGGAUGUCCUGGCCUGGGGGAAACUGAAAGAUAUGUGGGCAUAGUCAGUGGGUAGCAGGGCGUUUCAAAACGAAGGUAGUGCA-UACACACAUACAUAUGUA
.((..(((((((.((....)))))))))..))..........((((((((((...))).(((.((((((..((.((((.....))))))..))).-))).)))...))))))). ( -33.60)
>consensus
GCCAACGGGUUAAGGAUGUCCUGGCCUGGGGAAAACUGAAAGAUAUGUGGGCAUAGUCAGUGGGUAGCAGGGCGUUUCAAAACGAAGGUAGUGCA_UACAUACAUACAUACAUA
(((..((..((...(((((((((((((.......(((((....((((....)))).)))))))))..)))))))))..))..))..)))......................... (-27.68 = -27.93 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:27 2006