Locus 1604

Sequence ID	X_DroMel_CAF1
Location	4,601,842 – 4,602,037
Length	195
Max. P	0.964679

overview

Window 5

Location	4,601,842 – 4,601,960
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.45
Mean single sequence MFE	-26.41
Consensus MFE	-18.75
Energy contribution	-19.62
Covariance contribution	0.87
Combinations/Pair	1.13
Mean z-score	-1.63
Structure conservation index	0.71
SVM decision value	0.21
SVM RNA-class probability	0.633612
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4601842 118 + 22224390
UAUAAUUAACGGCAAUAAAAAUCAAAGCCUGCGGAAGU--CUUCAAUUUAAGUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGA
..........(((.............))).......((--((((.(((((((....(((((..(((..((((((.....))))))..))))))))...)))))))....))))))..... ( -27.22)
>DroSec_CAF1 26838 118 + 1
AAUAAUUAACGGAAAUAAGAAUCAAAGCCUGCGGAAGU--CUUCAAUUUAUUUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGA
..........(((((((((...........((....))--..(((.(((((((..((((.....))))..)))))))))))))))))))..((....))...((((.(....).)))).. ( -29.50)
>DroEre_CAF1 29825 110 + 1
---------CGAAUAUAGACAUCAAAGUCUGAGGAAGACCGAAGAAUU-AUGUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUAA
---------.......((((......))))(((((....((((.(...-.).))))(((((..(((..((((((.....))))))..)))))))).))))).((((.(....).)))).. ( -27.70)
>DroYak_CAF1 28322 111 + 1
-----UU--AGAAUAUAAAAAUCAAAGUCUGAGAAAGC--CAUGAAUUAAUGUUCGAACUAAUUGGUCAUAAGUGAAUGACUUAUUGCCAUGGAUAUCCUUGAAUGACGGAAGGCAUUGA
-----..--............((((.((((.......(--(((((((....)))).........(((.((((((.....)))))).)))))))...(((.........))))))).)))) ( -21.20)
>consensus
_____UU__CGAAAAUAAAAAUCAAAGCCUGAGGAAGU__CAUCAAUUUAUGUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGA
.........((((((((((.........((.....)).........))))))))))(((((..(((..((((((.....))))))..)))))))).......((((.(....).)))).. (-18.75 = -19.62 +   0.87)

alignment

secondary structure

dotplot

Window 6

Location	4,601,880 – 4,601,997
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	93.08
Mean single sequence MFE	-33.75
Consensus MFE	-30.66
Energy contribution	-30.72
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.91
SVM decision value	1.57
SVM RNA-class probability	0.964679
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4601880 117 + 22224390
CUUCAAUUUAAGUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGAAAUGGUCCUGCAAAUUGGCUCGUUUGGAUUGC--GCCAA
...........((.((((((((.((((((....((...((((.(((((((.((....)).))((((.(....).)))))))))))))...))...)))).)).)))))))).--))... ( -30.80)
>DroSec_CAF1 26876 117 + 1
CUUCAAUUUAUUUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGC--GCCAA
..(((.(((((((..((((.....))))..))))))))))..........(((..((((...((((.(....).)))).(((((((((........)))))))))))))...--.))). ( -35.00)
>DroEre_CAF1 29856 116 + 1
GAAGAAUU-AUGUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUAAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGC--GCCAA
...((((.-..))))........(((..((((((.....))))))..)))(((..((((...((((.(....).)))).(((((((((........)))))))))))))...--.))). ( -34.30)
>DroYak_CAF1 28353 119 + 1
CAUGAAUUAAUGUUCGAACUAAUUGGUCAUAAGUGAAUGACUUAUUGCCAUGGAUAUCCUUGAAUGACGGAAGGCAUUGAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGCGCGCCAA
...........((((((......((((.((((((.....)))))).)))).((....))))))))...((...(((((.(((((((((........))))))))).)).)))...)).. ( -34.90)
>consensus
CAUCAAUUUAUGUUCGAUCUAAUUGGUCAUAAGUGAAUGACUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGC__GCCAA
.......................(((..((((((.....))))))..)))(((..((((...((((.(....).)))).(((((((((........)))))))))))))......))). (-30.66 = -30.72 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	4,601,920 – 4,602,037
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	95.76
Mean single sequence MFE	-29.60
Consensus MFE	-27.41
Energy contribution	-27.10
Covariance contribution	-0.31
Combinations/Pair	1.09
Mean z-score	-1.49
Structure conservation index	0.93
SVM decision value	0.09
SVM RNA-class probability	0.579864
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4601920 117 + 22224390
CUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGAAAUGGUCCUGCAAAUUGGCUCGUUUGGAUUGC--GCCAACACAGUUCCCAUUAAAAUUGACUUCAAGUUAUUUACAUAG
..........((((((..(((((((((((.(....(((.(((((..((........))..))))).)))).)--))))...(((((........)))))..)))))).))))))..... ( -24.00)
>DroSec_CAF1 26916 117 + 1
CUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGC--GCCAACACAAUUCCCAUUAAAAUUGACUUCAAGUUAUUUACAUAG
..........((((((..(((((((((((.(....(((.(((((((((........))))))))).)))).)--))))...(((((........)))))..)))))).))))))..... ( -31.40)
>DroEre_CAF1 29895 117 + 1
CUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUAAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGC--GCCAACGCAAUUCCCAUUAAAAUUGACUUCAAGUUAUUUACAUAG
..........((((((..((((((((.(....).))...(((((((((........)))))))))(((((((--(....))))))))..............)))))).))))))..... ( -32.50)
>DroYak_CAF1 28393 119 + 1
CUUAUUGCCAUGGAUAUCCUUGAAUGACGGAAGGCAUUGAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGCGCGCCAACACAAUUCCCAUUGAAAUUGACUUCAAGUUAUUUACAUAG
...........((....)).((((((((.(((((((((.(((((((((........))))))))).)).))).........(((((........))))).))))..))))))))..... ( -30.50)
>consensus
CUUAUUUCCAUGGAUAUCCUUGAAUGGCGGAAGGCAUUGAAAUGAGCCUGCAAAUUGGCUCGUUUGGAUUGC__GCCAACACAAUUCCCAUUAAAAUUGACUUCAAGUUAUUUACAUAG
..........((((((..((((((((..((...(((((.(((((((((........))))))))).)).)))...))..))(((((........)))))..)))))).))))))..... (-27.41 = -27.10 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:29 2006