Locus 1094

Sequence ID X_DroMel_CAF1
Location 3,219,284 – 3,219,420
Length 136
Max. P 0.919709
window1773 window1774

overview

Window 3

Location 3,219,284 – 3,219,382
Length 98
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 94.92
Mean single sequence MFE -22.88
Consensus MFE -19.79
Energy contribution -20.35
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.33
Structure conservation index 0.87
SVM decision value 1.13
SVM RNA-class probability 0.919709
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3219284 98 + 22224390
CACCAUCGCCUAUCUUGCCCUCUCUGC-UUUCCCAUAUUCCUUCGCCUUCUGGGCGCGUGGGAAAAUAGAAACUCAACCGCAGAGUUUAAUUUCGUUUU
.....................((((((-((((((((.......((((.....)))).))))))))...(.....)....)))))).............. ( -22.10)
>DroSec_CAF1 28307 97 + 1
CUCCAUCGCCUAUCUGGCCCUCUCUUU-UUUCCCAUAUUCCUUCGCCUUCUGUGCGCGUGGGAAAAUAGAAACUCAACCGCAGAGUUUUAUUUCGUUU-
.......(((.....)))....(((.(-((((((((.......((((....).))).))))))))).)))(((((.......)))))...........- ( -21.60)
>DroEre_CAF1 30218 98 + 1
CUCCAUCGCCUAUCUGGCCCUCACUUU-UUUCCCAUAUUCCUUCGCCUUCUGGGCGCGUGGGAAAAUAGAAACUUAACCGCAGAGUUUUAUUUCGUUUU
.......(((.....))).....((.(-((((((((.......((((.....)))).))))))))).))((((((.......))))))........... ( -22.90)
>DroYak_CAF1 33525 99 + 1
CUCCAUCGCCUAUCUGGCCCUCUCUUUUUUUCCCAUAUUCCUUCGCCUUCUGGGCGCGUGGGAAAAUAGAAACUCAACCGCAGAGUUUUAUUUCGUUUU
.......(((.....))).........(((((((((.......((((.....)))).)))))))))..(((((((.......))))))).......... ( -24.90)
>consensus
CUCCAUCGCCUAUCUGGCCCUCUCUUU_UUUCCCAUAUUCCUUCGCCUUCUGGGCGCGUGGGAAAAUAGAAACUCAACCGCAGAGUUUUAUUUCGUUUU
.......(((.....)))..........((((((((.......((((.....)))).))))))))...(((((((.......))))))).......... (-19.79 = -20.35 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 4

Location 3,219,307 – 3,219,420
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -19.16
Consensus MFE -12.74
Energy contribution -13.26
Covariance contribution 0.52
Combinations/Pair 1.10
Mean z-score -1.62
Structure conservation index 0.66
SVM decision value 0.08
SVM RNA-class probability 0.574267
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3219307 113 - 22224390
CUCAAAACAGAAAAAACAAAAAACACGAGCAAAAUAA--CAAAACGAAAUUAAACUCUGCGGUUGAGUUUCUAUUUUCCCACGCGCCCAGAAGGCGAAGGAAUAUGGGAAA-GCAG----
(((((..((((..........................--................))))...)))))(((((((.((((....((((.....))))..)))).))))))).-....---- ( -21.35)
>DroSec_CAF1 28330 98 - 1
CUCAA--CAG----------AAACACGAGCAAAAUA-----AAACGAAAUAAAACUCUGCGGUUGAGUUUCUAUUUUCCCACGCGCACAGAAGGCGAAGGAAUAUGGGAAA-AAAG----
(((((--(..----------...((.(((.......-----.............)))))..))))))(((((((.((((..(((.(......))))..)))).))))))).-....---- ( -20.05)
>DroEre_CAF1 30241 103 - 1
CUCAA--CAA----------AAACACGAGCAAAAUAAAAUAAAACGAAAUAAAACUCUGCGGUUAAGUUUCUAUUUUCCCACGCGCCCAGAAGGCGAAGGAAUAUGGGAAA-AAAG----
.....--...----------.........................(((((..((((....))))..)))))..((((((((..((((.....))))........)))))))-)...---- ( -17.80)
>DroYak_CAF1 33548 102 - 1
CUCAA--CAA----------AAACACGAGCAAAAUAA--CAAAACGAAAUAAAACUCUGCGGUUGAGUUUCUAUUUUCCCACGCGCCCAGAAGGCGAAGGAAUAUGGGAAAAAAAG----
(((((--(..----------...((.(((........--...............)))))..))))))(((((((.((((....((((.....))))..)))).)))))))......---- ( -22.40)
>DroAna_CAF1 45449 102 - 1
AAAUA--CAA----------AAUAA---GGGAAAAAA--CAAAACGAUAUACAACUUUGCGGUUGAGUUUCUAUUUUCCCACGCGCUGAGGAGGUGAAGAAAUAAGAGAAA-AAUAAAAC
.....--...----------.....---(((((((..--..((((......(((((....))))).))))...)))))))...((((.....))))...............-........ ( -14.20)
>consensus
CUCAA__CAA__________AAACACGAGCAAAAUAA__CAAAACGAAAUAAAACUCUGCGGUUGAGUUUCUAUUUUCCCACGCGCCCAGAAGGCGAAGGAAUAUGGGAAA_AAAG____
.............................................(((((..((((....))))..)))))...(((((((..((((.....))))........)))))))......... (-12.74 = -13.26 +   0.52) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:25 2006