Locus 223

Sequence ID	3R_DroMel_CAF1
Location	888,820 – 888,956
Length	136
Max. P	0.999919

overview

Window 2

Location	888,820 – 888,922
Length	102
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	74.07
Mean single sequence MFE	-26.43
Consensus MFE	-16.21
Energy contribution	-15.66
Covariance contribution	-0.55
Combinations/Pair	1.16
Mean z-score	-3.15
Structure conservation index	0.61
SVM decision value	4.55
SVM RNA-class probability	0.999919
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 888820 102 - 27905053
GUGUUGAGUGUUUUAUUAAUUAAAGUGCUUAACU-CACUAUGGCUAUUGCUAUUGCUAUGAUGGCUAUGGCUAUGGCUUUGGCUCUUGGUUGCAGUUGUUGUU
(.((((((..(((((.....)))))..)))))).-)((((.(((((..(((((.((((((.....)))))).)))))..)))))..))))............. ( -33.10)
>DroPse_CAF1 64541 91 - 1
GUGUUGAGCGUUUUAUUAAUUAAAGUGCUUAACUUUACUCUAGCUUUAGUU-------UUGUGGCUGUGACUGUGGCAGUGACA-GUGUUUGCUGUUAA----
..(((((((((((((.....))))))))))))).........(((.(((((-------..........))))).)))..(((((-((....))))))).---- ( -24.80)
>DroPer_CAF1 64420 85 - 1
GUGUUGAGCGUUUUAUUAAUUAAAGUGCUUAACUUUACUCUAGCUUUAGUU-------UUGUGGCUGUGACUGUGGCA-------GUGUUUGCUGUUAA----
..(((((((((((((.....))))))))))))).....(((((((......-------....))))).))...(((((-------((....))))))).---- ( -21.40)
>consensus
GUGUUGAGCGUUUUAUUAAUUAAAGUGCUUAACUUUACUCUAGCUUUAGUU_______UUGUGGCUGUGACUGUGGCA_UG_C__GUGUUUGCUGUUAA____
..(((((((..((((.....))))..))))))).........(((.(((((.................))))).))).......................... (-16.21 = -15.66 +  -0.55)

alignment

secondary structure

dotplot

Window 3

Location	888,860 – 888,956
Length	96
Sequences	3
Columns	97
Reading direction	forward
Mean pairwise identity	86.62
Mean single sequence MFE	-12.13
Consensus MFE	-9.83
Energy contribution	-9.83
Covariance contribution	0.01
Combinations/Pair	1.14
Mean z-score	-1.75
Structure conservation index	0.81
SVM decision value	0.03
SVM RNA-class probability	0.551029
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 888860 96 + 27905053
CAUCAUAGCAAUAGCAAUAGCCAUAGUG-AGUUAAGCACUUUAAUUAAUAAAACACUCAACACAGAACAAAUUGACUACUUGACUGGCAGCAACACA
.......((....((....))....((.-(((((((....((((((.......................))))))...))))))).)).))...... ( -12.20)
>DroPse_CAF1 64576 90 + 1
CACAA-------AACUAAAGCUAGAGUAAAGUUAAGCACUUUAAUUAAUAAAACGCUCAACACAAAACAAAUUGACUACUUGACUGGCAGCAAAACA
.....-------.......(((((((((..(((.(((..((((.....))))..))).))).(((......)))..))))...)))))......... ( -12.10)
>DroPer_CAF1 64449 90 + 1
CACAA-------AACUAAAGCUAGAGUAAAGUUAAGCACUUUAAUUAAUAAAACGCUCAACACAAAACAAAUUGACUACUUGACUGGCAGCAAAACA
.....-------.......(((((((((..(((.(((..((((.....))))..))).))).(((......)))..))))...)))))......... ( -12.10)
>consensus
CACAA_______AACUAAAGCUAGAGUAAAGUUAAGCACUUUAAUUAAUAAAACGCUCAACACAAAACAAAUUGACUACUUGACUGGCAGCAAAACA
...................(((((((((..(((.(((..((((.....))))..))).))).(((......)))..))))...)))))......... ( -9.83 =  -9.83 +   0.01)

alignment

secondary structure

dotplot

Window 4

Location	888,860 – 888,956
Length	96
Sequences	3
Columns	97
Reading direction	reverse
Mean pairwise identity	86.62
Mean single sequence MFE	-17.97
Consensus MFE	-16.63
Energy contribution	-15.97
Covariance contribution	-0.66
Combinations/Pair	1.13
Mean z-score	-1.07
Structure conservation index	0.93
SVM decision value	0.03
SVM RNA-class probability	0.548625
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 888860 96 - 27905053
UGUGUUGCUGCCAGUCAAGUAGUCAAUUUGUUCUGUGUUGAGUGUUUUAUUAAUUAAAGUGCUUAACU-CACUAUGGCUAUUGCUAUUGCUAUGAUG
...((((((((.......)))).))))......((.((((((..(((((.....)))))..)))))).-)).((((((..........))))))... ( -21.70)
>DroPse_CAF1 64576 90 - 1
UGUUUUGCUGCCAGUCAAGUAGUCAAUUUGUUUUGUGUUGAGCGUUUUAUUAAUUAAAGUGCUUAACUUUACUCUAGCUUUAGUU-------UUGUG
......((((.(((.(((((.....)))))..))).(((((((((((((.....))))))))))))).......)))).......-------..... ( -16.10)
>DroPer_CAF1 64449 90 - 1
UGUUUUGCUGCCAGUCAAGUAGUCAAUUUGUUUUGUGUUGAGCGUUUUAUUAAUUAAAGUGCUUAACUUUACUCUAGCUUUAGUU-------UUGUG
......((((.(((.(((((.....)))))..))).(((((((((((((.....))))))))))))).......)))).......-------..... ( -16.10)
>consensus
UGUUUUGCUGCCAGUCAAGUAGUCAAUUUGUUUUGUGUUGAGCGUUUUAUUAAUUAAAGUGCUUAACUUUACUCUAGCUUUAGUU_______UUGUG
......((((.(((.(((((.....)))))..))).(((((((..((((.....))))..))))))).......))))................... (-16.63 = -15.97 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:05 2006