Locus 166

Sequence ID	3R_DroMel_CAF1
Location	823,523 – 823,643
Length	120
Max. P	0.998666

overview

Window 5

Location	823,523 – 823,643
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.49
Mean single sequence MFE	-25.48
Consensus MFE	-23.10
Energy contribution	-23.54
Covariance contribution	0.44
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.91
SVM decision value	3.18
SVM RNA-class probability	0.998666
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 823523 120 + 27905053
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAAUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUCUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUGG
......(((....)))(((...((((((((((((...(((.....)))((.(((....)))..))....................))))))))))))....)))................ ( -27.10)
>DroSec_CAF1 5885 120 + 1
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAGUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGCUUUGAUAUCUCGCUGGAAAAAACCUCUGGCUUAAAUUUAUAUUUUG
......(((....)))((((..((((((((((((..((((.....))))....((((..((...........))..)))).....))))))))))))...))))................ ( -27.40)
>DroSim_CAF1 3062 120 + 1
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAAUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGCUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUUG
......(((....)))(((...((((((((((((..((((.....))))....((((..((...........))..)))).....))))))))))))....)))................ ( -27.40)
>DroEre_CAF1 6492 118 + 1
UUUUUUCCCAUUUCAGGUUAUUGUU--UUCCAGCCACGAGUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUUG
......(((.....(((((....((--(((((((...(((......((((.(((....((......))...))).))))...))))))))))))))))).)))................. ( -23.40)
>DroYak_CAF1 6180 117 + 1
UUUUUUU-CAUUUGGGGUAAUGGUUU-UUUCAGCUACGAGUCGUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAUAUUUAUAUUUU-
.......-..((((((((.....(((-(((((((..((((.....))))....((((.((...........))...)))).....))))))))))))))))))................- ( -22.10)
>consensus
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAGUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUUG
.........(((((((.(....((((((((((((..((((.....))))....((((.((...........))...)))).....))))))))))))....).))))))).......... (-23.10 = -23.54 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	823,523 – 823,643
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.49
Mean single sequence MFE	-25.76
Consensus MFE	-20.70
Energy contribution	-21.50
Covariance contribution	0.80
Combinations/Pair	1.08
Mean z-score	-3.34
Structure conservation index	0.80
SVM decision value	2.79
SVM RNA-class probability	0.997034
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 823523 120 - 27905053
CCAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAGAACGAAACAAGGAAACGAUGACGUACCGAAAAAGAUUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...(((((.(..(....).....((...)).....).))))).))))))))))))......(((....)))...... ( -27.70)
>DroSec_CAF1 5885 120 - 1
CAAAAUAUAAAUUUAAGCCAGAGGUUUUUUCCAGCGAGAUAUCAAAGCGAAACAAGGAAACGAUGACGUACCGAAAAAGACUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...((((.....(....).....((...))........)))).))))))))))))......(((....)))...... ( -26.70)
>DroSim_CAF1 3062 120 - 1
CAAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAGCGAAACAAGGAAACGAUGACGUACCGAAAAAGAUUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...(((((.(..(....).....((...)).....).))))).))))))))))))......(((....)))...... ( -28.00)
>DroEre_CAF1 6492 118 - 1
CAAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAACGAAACAAGGAAACGAUGACGUACCGAAAAAGACUCGUGGCUGGAA--AACAAUAACCUGAAAUGGGAAAAAA
.................((((((((((((((((((...........(((......(....).....))).((((.......))).))))))))--))....)))))....))))...... ( -25.30)
>DroYak_CAF1 6180 117 - 1
-AAAAUAUAAAUAUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAACGAAACAAGGAAACGAUGACGUACCGAAAACGACUCGUAGCUGAAA-AAACCAUUACCCCAAAUG-AAAAAAA
-.....................(((((((((.(((((....))...((((.....(....).....(((.......)))..)))).)))))))-))))).............-....... ( -21.10)
>consensus
CAAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAACGAAACAAGGAAACGAUGACGUACCGAAAAAGACUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...((((.....(....).....((...))........)))).)))))))))))).....(((.....)))...... (-20.70 = -21.50 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:32 2006