Locus 3422

Sequence ID	3L_DroMel_CAF1
Location	10,048,270 – 10,048,360
Length	90
Max. P	0.984116

overview

Window 9

Location	10,048,270 – 10,048,360
Length	90
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	76.55
Mean single sequence MFE	-18.38
Consensus MFE	-11.00
Energy contribution	-10.62
Covariance contribution	-0.39
Combinations/Pair	1.42
Mean z-score	-1.69
Structure conservation index	0.60
SVM decision value	0.65
SVM RNA-class probability	0.811390
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10048270 90 + 23771897
CACUAAGUUUGUUGUUUGGCUUUUGCGCCAUGAUUGUCGUCAAAGUAUUGUAAAACAACAAAUGACAUGAGCGAACAACAAAAGCAA-------AAA
.......((((((((((((((((.(((.((....)).))).))))).((((......))))..........))))))))))).....-------... ( -20.60)
>DroSec_CAF1 93169 84 + 1
CACUAAGUUUGUUGUUUGGUUUUUGCGCCAUGAUUGUCGCCACAGUAUUGUAAAACUA-AAAUGACAUGAACAAACAACAACA-----------AA-
......(((.((((((((......(((.((....)).)))...(((........))).-............))))))))))).-----------..- ( -15.30)
>DroSim_CAF1 103076 86 + 1
CACUAAGUUUGUUGUUUGGUUUUUGUGCCAUGAUUGUCGCCACAGUAUUGUAAAACAACAAAUGACAUGAACAAACAACAACA-----------AAA
......(((.((((((((...((..((.(((.(((((....))))).((((......))))))).))..))))))))))))).-----------... ( -17.40)
>DroEre_CAF1 97611 97 + 1
CACUGAGUUUGUUGUUUGUCUUUUGCGCCAUGAUUGUCGCCACAGUAUUGUAAAACAACAAAUGACAUGGGCGAAAAACAAAAAAGAAAAACCAAAG
...((.((((.((.(((((.((((((.((((((((((....))))).((((......))))....))))))))))).)))))...)).))))))... ( -23.40)
>DroYak_CAF1 97974 83 + 1
CACUGAGUUUGUUGUUUGUCUUUUGCGCCAUGAUUGUCGCCACAGUAUUGUAAAACAACAAAUGACACGAGCAAAAAACAAAA--------------
......((((.((((((((.....(((.((....)).)))....((.((((......))))...)))))))))).))))....-------------- ( -15.70)
>DroAna_CAF1 94376 77 + 1
UGC----AUUGUUGUUUGUCUUUUGUGCAGUGAUUGUUGCCGCAAUAUUGUGUGACGACAA-CAACACUC-UAAAUCAUAACA--------------
...----..(((((((.(((..(..(((((((.((((....)))))))))))..).)))))-)))))...-............-------------- ( -17.90)
>consensus
CACUAAGUUUGUUGUUUGGCUUUUGCGCCAUGAUUGUCGCCACAGUAUUGUAAAACAACAAAUGACAUGAGCAAACAACAAAA___________AA_
........((((((((((......(((.((....)).))).......((((......))))..........))))))))))................ (-11.00 = -10.62 +  -0.39)

alignment

secondary structure

dotplot

Window 0

Location	10,048,270 – 10,048,360
Length	90
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	76.55
Mean single sequence MFE	-21.72
Consensus MFE	-11.83
Energy contribution	-12.25
Covariance contribution	0.42
Combinations/Pair	1.36
Mean z-score	-2.60
Structure conservation index	0.54
SVM decision value	1.96
SVM RNA-class probability	0.984116
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10048270 90 - 23771897
UUU-------UUGCUUUUGUUGUUCGCUCAUGUCAUUUGUUGUUUUACAAUACUUUGACGACAAUCAUGGCGCAAAAGCCAAACAACAAACUUAGUG
...-------..((((((((((((......(((((..(((((.....)))))...))))).......((((......)))))))))))))...))). ( -21.90)
>DroSec_CAF1 93169 84 - 1
-UU-----------UGUUGUUGUUUGUUCAUGUCAUUU-UAGUUUUACAAUACUGUGGCGACAAUCAUGGCGCAAAAACCAAACAACAAACUUAGUG
-..-----------..((((((((((....((((((..-(.((((((((....))))).))).)..)))))).......))))))))))........ ( -16.70)
>DroSim_CAF1 103076 86 - 1
UUU-----------UGUUGUUGUUUGUUCAUGUCAUUUGUUGUUUUACAAUACUGUGGCGACAAUCAUGGCACAAAAACCAAACAACAAACUUAGUG
.((-----------(((((((.((((((((((....(((((((..((((....))))))))))).))))).))))).....)))))))))....... ( -23.80)
>DroEre_CAF1 97611 97 - 1
CUUUGGUUUUUCUUUUUUGUUUUUCGCCCAUGUCAUUUGUUGUUUUACAAUACUGUGGCGACAAUCAUGGCGCAAAAGACAAACAACAAACUCAGUG
..(((((((...((.(((((((((.(((((((....(((((((..((((....))))))))))).))))).)).))))))))).)).)))).))).. ( -26.00)
>DroYak_CAF1 97974 83 - 1
--------------UUUUGUUUUUUGCUCGUGUCAUUUGUUGUUUUACAAUACUGUGGCGACAAUCAUGGCGCAAAAGACAAACAACAAACUCAGUG
--------------.(((((((((((((((((....(((((((..((((....))))))))))).))))).)))))))))))).............. ( -25.30)
>DroAna_CAF1 94376 77 - 1
--------------UGUUAUGAUUUA-GAGUGUUG-UUGUCGUCACACAAUAUUGCGGCAACAAUCACUGCACAAAAGACAAACAACAAU----GCA
--------------((((........-.(((((((-((((((.((........))))))))))).))))........)))).........----... ( -16.63)
>consensus
_UU___________UGUUGUUGUUUGCUCAUGUCAUUUGUUGUUUUACAAUACUGUGGCGACAAUCAUGGCGCAAAAGACAAACAACAAACUUAGUG
................(((((.((((((((((....((((((((.((......)).)))))))).))))).))))).....)))))........... (-11.83 = -12.25 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:48 2006