Locus 1382

Sequence ID	X_DroMel_CAF1
Location	4,120,577 – 4,120,766
Length	189
Max. P	0.855598

overview

Window 4

Location	4,120,577 – 4,120,693
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.82
Mean single sequence MFE	-29.97
Consensus MFE	-28.27
Energy contribution	-27.83
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.97
Structure conservation index	0.94
SVM decision value	0.81
SVM RNA-class probability	0.855598
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4120577 116 - 22224390
AAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGACCCUUUAACCUGGGACCCACAAGCCAGGAAAAGGAGCCAACACCCGACACUUGUAAAUUUCUUAUGAGCACCAAUGCAAAAA----
..(((.(((((.(((......((((((..((((..(((((..(((((..........))))).)))))..))))...)))).....))......))).))))).))).........---- ( -29.10)
>DroSim_CAF1 7490 120 - 1
AAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGGCCCUUUAACCUGGGACCCACAAGCCAGGAAAAGGAGCCAACACCCGACACUUGUAAAUUUCUUAUGAGCACCAAUGCGAAAAACAA
..(((.(((((...(((((...(((((.(((((((((........))).))))..)))))))....))))).........((....))..........))))).)))............. ( -32.10)
>DroYak_CAF1 8692 115 - 1
AAUGGAGUUCAAGAGCUUCAGACUUGGACUUGGAACCUUUAACCUGGGACUCACAAGCCAGGAAAAGGAGCCAACACCUGACACUUGUAAAUUUCUUAUGAGCACCAAUGCAAAA-----
..(((((((....)))))))(..((((..((((..(((((..(((((..........))))).)))))..)))).........((..(((.....)))..))..))))..)....----- ( -28.70)
>consensus
AAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGACCCUUUAACCUGGGACCCACAAGCCAGGAAAAGGAGCCAACACCCGACACUUGUAAAUUUCUUAUGAGCACCAAUGCAAAAA____
..(((.(((((.(((......((((((..((((..(((((..(((((..........))))).)))))..))))...)))).....))......))).))))).)))............. (-28.27 = -27.83 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	4,120,613 – 4,120,731
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.18
Mean single sequence MFE	-39.67
Consensus MFE	-34.81
Energy contribution	-34.70
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.96
Structure conservation index	0.88
SVM decision value	0.33
SVM RNA-class probability	0.690609
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4120613 118 - 22224390
--AAGUAGCAAGUUCAAGGGGCAGGGGUCACCUAAGGCUGAAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGACCCUUUAACCUGGGACCCACAAGCCAGGAAAAGGAGCCAACACCCG
--.......(((((((((.(((.(((....)))...)))...((((((......))))))..)))))))))((..(((((..(((((..........))))).)))))..))........ ( -37.00)
>DroSim_CAF1 7530 118 - 1
--AAGUAGCAAGUUCAAGGGGCAGGGGUUACCUAAGGCUGAAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGGCCCUUUAACCUGGGACCCACAAGCCAGGAAAAGGAGCCAACACCCG
--......((((((((((.(((.(((....)))...)))...((((((......))))))..))))))))))((((((((..(((((..........))))).))))).)))........ ( -42.80)
>DroYak_CAF1 8727 120 - 1
GCAAGUAGCAAGUUCAAGGGGCAGGGGCCAUUGCUGGCUGAAUGGAGUUCAAGAGCUUCAGACUUGGACUUGGAACCUUUAACCUGGGACUCACAAGCCAGGAAAAGGAGCCAACACCUG
((......((((((((((.......(((((....)))))...(((((((....)))))))..))))))))))...(((((..(((((..........))))).))))).))......... ( -39.20)
>consensus
__AAGUAGCAAGUUCAAGGGGCAGGGGUCACCUAAGGCUGAAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGACCCUUUAACCUGGGACCCACAAGCCAGGAAAAGGAGCCAACACCCG
.........(((((((((.(((.(((....)))...)))...(((((((....)))))))..)))))))))((..(((((..(((((..........))))).)))))..))........ (-34.81 = -34.70 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	4,120,653 – 4,120,766
Length	113
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	86.97
Mean single sequence MFE	-38.30
Consensus MFE	-30.83
Energy contribution	-30.50
Covariance contribution	-0.33
Combinations/Pair	1.09
Mean z-score	-1.82
Structure conservation index	0.80
SVM decision value	0.08
SVM RNA-class probability	0.571302
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4120653 113 - 22224390
CAAGCGGACUAACAGUUGCAACUUGAAGCUGUUGC-------AAGUAGCAAGUUCAAGGGGCAGGGGUCACCUAAGGCUGAAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGACCCUUU
.(((.((......(.(((((((........)))))-------)).)..((((((((((.(((.(((....)))...)))...((((((......))))))..))))))))))..))))). ( -36.80)
>DroSim_CAF1 7570 111 - 1
CGAGCGGACCAACAGUUGCA--CUGAAGCUGUUGC-------AAGUAGCAAGUUCAAGGGGCAGGGGUUACCUAAGGCUGAAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGGCCCUUU
.(((.((.(((((((((...--....)))))))..-------......((((((((((.(((.(((....)))...)))...((((((......))))))..))))))))))))))))). ( -37.70)
>DroYak_CAF1 8767 120 - 1
CGAGCUGACUAACAGUUGCAACUUGAAGCUGUUGCAAGUUGCAAGUAGCAAGUUCAAGGGGCAGGGGCCAUUGCUGGCUGAAUGGAGUUCAAGAGCUUCAGACUUGGACUUGGAACCUUU
.(((((..(((....((((((((((.........)))))))))).)))..)))))((((..(...(((((....))))).....(((((((((.........))))))))).)..)))). ( -40.40)
>consensus
CGAGCGGACUAACAGUUGCAACUUGAAGCUGUUGC_______AAGUAGCAAGUUCAAGGGGCAGGGGUCACCUAAGGCUGAAUGGAGUUCAAAAGCUUCAGACUUGGACUUGGACCCUUU
.........((((((((.(.....).))))))))..............((((((((((.(((.(((....)))...)))...(((((((....)))))))..))))))))))........ (-30.83 = -30.50 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:58 2006