Locus 473

Sequence ID	3L_DroMel_CAF1
Location	1,343,014 – 1,343,147
Length	133
Max. P	0.980620

overview

Window 9

Location	1,343,014 – 1,343,111
Length	97
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	84.24
Mean single sequence MFE	-33.37
Consensus MFE	-27.51
Energy contribution	-28.07
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.47
Structure conservation index	0.82
SVM decision value	-0.03
SVM RNA-class probability	0.520371
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1343014 97 + 23771897
GAGACCGGGCGGCUGGAUAGCAG---CAGCAGUAUCUGAUGGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAGUGCACCCACCUGCCCACCUG-------
.(((....((.((((.....)))---).))....)))...(((((.((((.........((.((((((((........)))))))))))))).)))))..------- ( -37.40)
>DroSim_CAF1 15259 104 + 1
GAGACCAGGCGGCAGGAUAGCAG---CAGCAGUAUCUGAUGGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAAUGCACCCACCCGCCCACCUGCCCACCU
......(((.((((((...((.(---(((.((((((((((....)))))....)))))))))((((((............)))))).....))...))))))..))) ( -32.10)
>DroEre_CAF1 15636 91 + 1
GAGACCAGGCAGCCGGAUAGCAGCAGCAGCAGUAUCUGAUGGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAGUGCACCCACCU----------------
(((.((.(((.((((((((.(.((....)).))))))...))).))).)))))......((.((((((((........))))))))))...---------------- ( -30.60)
>consensus
GAGACCAGGCGGCAGGAUAGCAG___CAGCAGUAUCUGAUGGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAGUGCACCCACCUGCCCACCUG_______
(((.((.(((.((((((((((.......))..)))))...))).))).)))))......((.((((((((........))))))))))................... (-27.51 = -28.07 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	1,343,014 – 1,343,111
Length	97
Sequences	3
Columns	107
Reading direction	reverse
Mean pairwise identity	84.24
Mean single sequence MFE	-36.83
Consensus MFE	-25.76
Energy contribution	-27.10
Covariance contribution	1.34
Combinations/Pair	1.10
Mean z-score	-2.45
Structure conservation index	0.70
SVM decision value	0.79
SVM RNA-class probability	0.852342
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1343014 97 - 23771897
-------CAGGUGGGCAGGUGGGUGCACUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACCAUCAGAUACUGCUG---CUGCUAUCCAGCCGCCCGGUCUC
-------..(((((.(((((.((((((((........)))))))).((.....)).))))).)))))...((((...((.(---(((.....)))).))...)))). ( -40.60)
>DroSim_CAF1 15259 104 - 1
AGGUGGGCAGGUGGGCGGGUGGGUGCAUUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACCAUCAGAUACUGCUG---CUGCUAUCCUGCCGCCUGGUCUC
((((((.(((((((.(((((.((((((((........)))))))).((.....)).))))).)))))....((((..((..---..)))))).))))))))...... ( -40.30)
>DroEre_CAF1 15636 91 - 1
----------------AGGUGGGUGCACUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACCAUCAGAUACUGCUGCUGCUGCUAUCCGGCUGCCUGGUCUC
----------------.((((((((((((........))))))))((.........)).....))))...((((...((.((((........)))).))...)))). ( -29.60)
>consensus
_______CAGGUGGGCAGGUGGGUGCACUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACCAUCAGAUACUGCUG___CUGCUAUCCAGCCGCCUGGUCUC
.........(((((.(((((.((((((((........)))))))).((.....)).))))).)))))....((((..((.......))))))..(((....)))... (-25.76 = -27.10 +   1.34)

alignment

secondary structure

dotplot

Window 1

Location	1,343,051 – 1,343,147
Length	96
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	85.57
Mean single sequence MFE	-33.05
Consensus MFE	-27.33
Energy contribution	-27.67
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.40
Structure conservation index	0.83
SVM decision value	1.87
SVM RNA-class probability	0.980620
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1343051 96 + 23771897
GGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAGUGCACCCACCUGCCCACCUG--------ACCACCCAUCGAAAAACCUGUUUACCUGGCCACGAA
((((((((((.........((.((((((((........))))))))))........))))--------))))))..(((.....((.........))...))). ( -34.43)
>DroSim_CAF1 15296 104 + 1
GGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAAUGCACCCACCCGCCCACCUGCCCACCUGGCCGCCCAUCGAAAAACCUGUUUACCUGGCCACGAA
(((((.((((.........((.((((((............))))))))........)))).)))))((((((.....((.......))......)))))).... ( -29.53)
>DroEre_CAF1 15676 88 + 1
GGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAGUGCACCCACCU----------------GGCCGCCCAUCGAAAAACCUGUUUACCUGGCCACCAA
((((((((((.........((.((((((((........))))))))))..(----------------((....)))................)))))))))).. ( -35.20)
>consensus
GGUGGUCAGGCUCAUAUUUUGCGGUGCACUAAUUAGAAAGUGCACCCACCUGCCCACCUG_______GGCCGCCCAUCGAAAAACCUGUUUACCUGGCCACGAA
.(((((((((.........((.((((((((........)))))))))).................................(((....))).)))))))))... (-27.33 = -27.67 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	1,343,051 – 1,343,147
Length	96
Sequences	3
Columns	104
Reading direction	reverse
Mean pairwise identity	85.57
Mean single sequence MFE	-38.92
Consensus MFE	-28.01
Energy contribution	-27.90
Covariance contribution	-0.11
Combinations/Pair	1.08
Mean z-score	-3.00
Structure conservation index	0.72
SVM decision value	1.20
SVM RNA-class probability	0.929711
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1343051 96 - 23771897
UUCGUGGCCAGGUAAACAGGUUUUUCGAUGGGUGGU--------CAGGUGGGCAGGUGGGUGCACUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACC
.(((.((((.(.....).))))...)))..((((((--------(((((...((..((((((((((........)))))))).)).....)).))))))))))) ( -42.80)
>DroSim_CAF1 15296 104 - 1
UUCGUGGCCAGGUAAACAGGUUUUUCGAUGGGCGGCCAGGUGGGCAGGUGGGCGGGUGGGUGCAUUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACC
....(((((.(.....)..((((......)))))))))(((((.(((((.......((((((((((........)))))))).))........))))).))))) ( -39.26)
>DroEre_CAF1 15676 88 - 1
UUGGUGGCCAGGUAAACAGGUUUUUCGAUGGGCGGCC----------------AGGUGGGUGCACUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACC
..(((((.(((((.....(((..((.....))..)))----------------...((((((((((........)))))))).))........))))).))))) ( -34.70)
>consensus
UUCGUGGCCAGGUAAACAGGUUUUUCGAUGGGCGGCC_______CAGGUGGGCAGGUGGGUGCACUUUCUAAUUAGUGCACCGCAAAAUAUGAGCCUGACCACC
...((((.(((((.....(((..((.....))..)))...................((((((((((........)))))))).))........))))).)))). (-28.01 = -27.90 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:51 2006