Locus 4913

Sequence ID X_DroMel_CAF1
Location 12,795,466 – 12,795,559
Length 93
Max. P 0.521435
window8012 window8013

overview

Window 2

Location 12,795,466 – 12,795,559
Length 93
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 82.83
Mean single sequence MFE -21.84
Consensus MFE -14.57
Energy contribution -14.47
Covariance contribution -0.10
Combinations/Pair 1.17
Mean z-score -1.76
Structure conservation index 0.67
SVM decision value -0.02
SVM RNA-class probability 0.521435
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12795466 93 + 22224390
UUUGUAUUUUAUUUU-------UUUCUGCCCUCGAGGGUGGCCAAAAGUUUAAUG-GGCAAAUCUGUUUAAUUAAAUGAUAAACAUUUAAUUUGCGCCGCC
....((((..(((((-------(..(..(((....)))..)..))))))..))))-(((......((..(((((((((.....))))))))).)))))... ( -20.80)
>DroEre_CAF1 2097 91 + 1
UUUGUAUUUUAUUUUUG---------UGCCUUCGAGGGCGCCCAAAAGUUUAAUG-UGCAAAUCUGUUUAAUUAAAUGAUAAACAUUUAAUUUGGGGCCGC
(((((((...(((((((---------(((((....))))))..)))))).....)-))))))...(((((((((((((.....)))))))))..))))... ( -19.90)
>DroYak_CAF1 1782 101 + 1
UUUGUAUUUUAUUUUUGUUAUUUUUCUGCCUUCGAGGGCAGGCAAAAGUUUGGUGGGGCAAAUCUGUUUAAUUAAAUGUUAAACAUUUAAUUUGGGUCGCC
..........((((((((.......((((((....))))))))))))))..(((((..(((((.((((((((.....))))))))....)))))..))))) ( -24.81)
>consensus
UUUGUAUUUUAUUUUUG_____UUUCUGCCUUCGAGGGCGGCCAAAAGUUUAAUG_GGCAAAUCUGUUUAAUUAAAUGAUAAACAUUUAAUUUGGGCCGCC
((((((((..(((((((........((((((....)))))).)))))))..)))...))))).......(((((((((.....)))))))))......... (-14.57 = -14.47 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,795,466 – 12,795,559
Length 93
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 82.83
Mean single sequence MFE -18.27
Consensus MFE -10.03
Energy contribution -10.37
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -2.69
Structure conservation index 0.55
SVM decision value -0.06
SVM RNA-class probability 0.505275
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12795466 93 - 22224390
GGCGGCGCAAAUUAAAUGUUUAUCAUUUAAUUAAACAGAUUUGCC-CAUUAAACUUUUGGCCACCCUCGAGGGCAGAAA-------AAAAUAAAAUACAAA
(((((.(((((((...((((((.........))))))))))))))-)......(....)))).(((....)))......-------............... ( -19.70)
>DroEre_CAF1 2097 91 - 1
GCGGCCCCAAAUUAAAUGUUUAUCAUUUAAUUAAACAGAUUUGCA-CAUUAAACUUUUGGGCGCCCUCGAAGGCA---------CAAAAAUAAAAUACAAA
...((((..(((((((((.....)))))))))....((.((((..-...))))))...))))(((......))).---------................. ( -15.60)
>DroYak_CAF1 1782 101 - 1
GGCGACCCAAAUUAAAUGUUUAACAUUUAAUUAAACAGAUUUGCCCCACCAAACUUUUGCCUGCCCUCGAAGGCAGAAAAAUAACAAAAAUAAAAUACAAA
(((((....(((((((((.....)))))))))........))))).........((((((((........))))))))....................... ( -19.50)
>consensus
GGCGACCCAAAUUAAAUGUUUAUCAUUUAAUUAAACAGAUUUGCC_CAUUAAACUUUUGGCCGCCCUCGAAGGCAGAAA_____CAAAAAUAAAAUACAAA
...(((...(((((((((.....)))))))))...((((((((......))))..)))))))(((......)))........................... (-10.03 = -10.37 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:55 2006