Locus 1198

Sequence ID	X_DroMel_CAF1
Location	3,569,566 – 3,569,767
Length	201
Max. P	0.923794

overview

Window 3

Location	3,569,566 – 3,569,677
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.43
Mean single sequence MFE	-47.94
Consensus MFE	-38.08
Energy contribution	-38.40
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-2.00
Structure conservation index	0.79
SVM decision value	1.16
SVM RNA-class probability	0.923794
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3569566 111 - 22224390
CAACUGCCGGUGAACGUCGCCAAAAACGCAGCUUCGACGUCCUCUGUCGCUGCCUCUACCGCAGCCGCUGCUGGCGUCGACUGCGGCAGCGAGGUCUCGC---------UGCCGAAAAGC
........((((.....))))......((((..((((((((..(.((.(((((.......))))).)).)..))))))))))))((((((((....))))---------))))....... ( -50.30)
>DroSec_CAF1 25798 111 - 1
CAACUGCCGGUGAACGUCGCCAAAAACGCAGCUUCGACGUCCUCUGUCGCUGCCUCUACCGCAGCCGCUGCUGACGUUGACUGCGGCAGCGAGACCUCGC---------UGCCGAAAAGC
.......((((.(((((((........(((((...((((.....))))(((((.......))))).)))))))))))).))))(((((((((....))))---------)))))...... ( -49.20)
>DroSim_CAF1 23157 111 - 1
CAACUGCCGGUGAACGUCGCCAAAAACGCAGCUUCGACGUCCUCUGUCGCUGCCUCUACCGCAGCCGCUGCUGACGUUGACUGCGGCAGCGAGGUUUCGC---------UGCCGAAAAGC
.......((((.(((((((........(((((...((((.....))))(((((.......))))).)))))))))))).))))((((((((......)))---------)))))...... ( -47.90)
>DroEre_CAF1 25568 120 - 1
CAACUGCCGGUGAACGUCGCCAAAAACGCAGCUUCGUCUUCCUCUGUCGCUGCCUCUGCCGCAGCCGCUGCUGGCGUCGACUGCGGCAGCGUGGUCUCGCGAAUGCUGCCGCCGAAAAGC
.....(((((((.....))))......(((((...(.(.......).)(((((.......))))).))))).))).(((...((((((((((.(.....)..)))))))))))))..... ( -46.50)
>DroYak_CAF1 27124 118 - 1
CAACUGCCGGUGAACGUCGCCAAAAACGCAGCUUCGUCUUCCUCAGUCGCUGCCUCUGCCGCAGCCGCUGCUGGCGUCGACUGCGGCAGCUGGGUUUCGCGAAUGCUGC--CCGAAAAGC
...(((((((((.....))))......(((((..((((.....((((.(((((.......))))).))))..))))..).))))))))).(((((...((....)).))--)))...... ( -45.80)
>consensus
CAACUGCCGGUGAACGUCGCCAAAAACGCAGCUUCGACGUCCUCUGUCGCUGCCUCUACCGCAGCCGCUGCUGGCGUCGACUGCGGCAGCGAGGUCUCGC_________UGCCGAAAAGC
...(((((((((.....))))......((((..((((((((..(.((.(((((.......))))).)).)..)))))))))))))))))............................... (-38.08 = -38.40 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	3,569,677 – 3,569,767
Length	90
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	91.47
Mean single sequence MFE	-22.30
Consensus MFE	-16.80
Energy contribution	-18.36
Covariance contribution	1.56
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.75
SVM decision value	0.38
SVM RNA-class probability	0.713728
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3569677 90 - 22224390
--GUUGUUUUUGUUGUUGUUGCUUAGAAGGCGAAAAAUCGGAAAAGACAAACAGGACAACUGCGAUAAACGACAACGAGAACGAACCGCUUA
--.((((((((((((((((((((.....))).....(((((......)...(((.....))))))).)))))))))))))))))........ ( -24.80)
>DroSec_CAF1 25909 90 - 1
--GCUGUUUUUGUUGUUGUUGCUUAGAAGGCGAAAAAUCGGAAAAGGCAAACAGGACAACUGCGAUAAACGACAACGAGAACGAACCGCUUA
--(((((((((((((((((((((.....))).....(((((......)...(((.....))))))).))))))))))))))))....))... ( -23.70)
>DroSim_CAF1 23268 90 - 1
--GCUGUUUUUGUUGUUGUUGCUUAGAAGGCGAAAAAUCGGAAAAGACAAACAGGACAACUGCGAUAAACGACAACGAGAACGAACCGCUUA
--(((((((((((((((((((((.....))).....(((((......)...(((.....))))))).))))))))))))))))....))... ( -23.50)
>DroEre_CAF1 25688 83 - 1
UU---------GUUGUUGCUGUUUAGAAGGCGAAAACUCGGAAAAGACAAACAGGACAACUGCGAUAAACGACAACGAGAACGAACCGCUUA
((---------.((((((.((((((...(.(((....)))...........(((.....))))..)))))).)))))).))........... ( -14.00)
>DroYak_CAF1 27242 92 - 1
CUGCUGUUGGUGUUGUUGUUGUUUAGAAGGCGAAAACUCGGAAAAGACAAACAGGACAACUGCGAUAAACGACAACGAGAACGAACCGCUUA
..((.(((.((.(((((((((((((...(.(((....)))...........(((.....))))..)))))))))))))..)).))).))... ( -25.50)
>consensus
__GCUGUUUUUGUUGUUGUUGCUUAGAAGGCGAAAAAUCGGAAAAGACAAACAGGACAACUGCGAUAAACGACAACGAGAACGAACCGCUUA
.....((((((((((((((((((.....)))....................(((.....))).....))))))))))))))).......... (-16.80 = -18.36 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:40 2006