Locus 5425

Sequence ID X_DroMel_CAF1
Location 14,153,695 – 14,153,822
Length 127
Max. P 0.996929
window8795 window8796 window8797

overview

Window 5

Location 14,153,695 – 14,153,792
Length 97
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 86.06
Mean single sequence MFE -34.88
Consensus MFE -30.65
Energy contribution -32.90
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -3.09
Structure conservation index 0.88
SVM decision value 2.77
SVM RNA-class probability 0.996929
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14153695 97 + 22224390
C------------UGCUGC-------UGCAUAAAUGCUGAAAGUUUCCUCCAAGGUAGCCUUGAUGUUGCCACUGCACUUUUUGUGCCGCAUGCCGCAGCAAAUUCCCCUUGCCUC
.------------((((((-------.(((....(((................((((((......))))))...((((.....)))).)))))).))))))............... ( -28.50)
>DroSec_CAF1 61727 104 + 1
C------------UGCUGCGGCGUUUCGCAUAAAUGCAGAAAGUUUCCUCCAAGGUAGCCUUGAUGUUUCCACUGCACUUUUUGUGCCGCAUGCCGCAGCAAAUUCCCCCUGCCUU
.------------(((((((((((...((((((((((((...........(((((...))))).((....)))))))...)))))))...)))))))))))............... ( -36.80)
>DroSim_CAF1 39482 101 + 1
---------------CUGCGGCGUUUCGCAUAAAUGCAGAAAGUUUCCUCCAAGGUAGCCUUGAUGUUGCCACUGCACUUUUUGUGCCGCAUGCCGCAGCAAAUUCCCCCUGCCAU
---------------(((((((((...((((((((((((..((....))....((((((......)))))).)))))...)))))))...)))))))))................. ( -34.00)
>DroEre_CAF1 53957 114 + 1
CUGCUACUGUUGCUGCUGCGGCGUUUCGCAUAAAUGCAGAAAGUUUCCUCCAAGGUAGCCUUGAUGUUGCCACUGCACUUUUUGUGCCGCAUGCCGCAGCAAAUUCCCCUCGCC--
..((.......))(((((((((((...((((((((((((..((....))....((((((......)))))).)))))...)))))))...))))))))))).............-- ( -40.20)
>consensus
C____________UGCUGCGGCGUUUCGCAUAAAUGCAGAAAGUUUCCUCCAAGGUAGCCUUGAUGUUGCCACUGCACUUUUUGUGCCGCAUGCCGCAGCAAAUUCCCCCUGCCUU
.............(((((((((((...((((((((((((..((....))....((((((......)))))).)))))...)))))))...)))))))))))............... (-30.65 = -32.90 +   2.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,153,695 – 14,153,792
Length 97
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 86.06
Mean single sequence MFE -36.38
Consensus MFE -31.62
Energy contribution -33.12
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.87
SVM decision value 1.82
SVM RNA-class probability 0.978786
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14153695 97 - 22224390
GAGGCAAGGGGAAUUUGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUUUCAGCAUUUAUGCA-------GCAGCA------------G
...............((((((.(((((..((((.....))))....((.....(((((...)))))(((....)))...))...))))).-------))))))------------. ( -31.40)
>DroSec_CAF1 61727 104 - 1
AAGGCAGGGGGAAUUUGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGAAACAUCAAGGCUACCUUGGAGGAAACUUUCUGCAUUUAUGCGAAACGCCGCAGCA------------G
...............(((((((((.....(((....((((((((((....)).(((((...)))))(((....))).)))))))).))).....)))))))))------------. ( -38.80)
>DroSim_CAF1 39482 101 - 1
AUGGCAGGGGGAAUUUGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUUUCUGCAUUUAUGCGAAACGCCGCAG---------------
..((((((.....))))))(((((.....(((....((((((((((....)).(((((...)))))(((....))).)))))))).))).....)))))..--------------- ( -34.20)
>DroEre_CAF1 53957 114 - 1
--GGCGAGGGGAAUUUGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUUUCUGCAUUUAUGCGAAACGCCGCAGCAGCAACAGUAGCAG
--.((....(....((((((((((.....(((....((((((((((....)).(((((...)))))(((....))).)))))))).))).....))))))))))...)....)).. ( -41.10)
>consensus
AAGGCAAGGGGAAUUUGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUUUCUGCAUUUAUGCGAAACGCCGCAGCA____________G
...............(((((((((.....(((....((((((((((....)).(((((...)))))(((....))).)))))))).))).....)))))))))............. (-31.62 = -33.12 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 14,153,716 – 14,153,822
Length 106
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 87.67
Mean single sequence MFE -37.43
Consensus MFE -27.38
Energy contribution -28.58
Covariance contribution 1.20
Combinations/Pair 1.09
Mean z-score -1.83
Structure conservation index 0.73
SVM decision value 0.33
SVM RNA-class probability 0.692503
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14153716 106 - 22224390
AAGUUGCGGGUU-----GGUUGGGCGUGGUGCGACGAGGCA-AGGGGAAUU--UGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUU
..(((((.....-----......(((((.(((.....((((-((.....))--))))))).))))).((((.....))))....)))))..(((((...)))))(((....))) ( -35.80)
>DroSec_CAF1 61755 106 - 1
AAGUUGCGGGCU-----GGUUGGGCGUGGCGCGGCAAGGCA-GGGGGAAUU--UGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGAAACAUCAAGGCUACCUUGGAGGAAACUU
......((((.(-----((((..(((((.(((((((((...-.......))--))))))).))))).((((.....)))).(((....)))...))))).))))(((....))) ( -40.40)
>DroSim_CAF1 39507 106 - 1
AAGUUGCGGGCU-----GGUUGGGCGUGGCGCGGCAUGGCA-GGGGGAAUU--UGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUU
..(((((.(.((-----......(((((.(((((((.....-.........--))))))).))))).((((.....))))))).)))))..(((((...)))))(((....))) ( -41.84)
>DroEre_CAF1 53997 101 - 1
AAGUUGCGGGUU-----GCUUGGACGUGGCGA-----GGCG-AGGGGAAUU--UGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUU
.........(((-----(((..(.((((.((.-----((((-((.....))--)))).)).))))).((((.....))))...))))))..(((((...)))))(((....))) ( -33.80)
>DroYak_CAF1 54668 109 - 1
AAGUUGCGAGUUCUGUUGGCUGGCAAGGGCGU-----GGCAAAGGGGAAUUUCUGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGUGGAAACUU
...((((.((((.....)))).))))..((((-----(.(..((.((.....)).))..).))))).((((.....))))(((.....((((((((...))))))))...))). ( -35.30)
>consensus
AAGUUGCGGGUU_____GGUUGGGCGUGGCGCG_C__GGCA_AGGGGAAUU__UGCUGCGGCAUGCGGCACAAAAAGUGCAGUGGCAACAUCAAGGCUACCUUGGAGGAAACUU
..(((((................(((((.(((.....(((((.((....)).)))))))).))))).((((.....))))....)))))..(((((...)))))(((....))) (-27.38 = -28.58 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:34 2006