Locus 48

Sequence ID	4_DroMel_CAF1
Location	421,236 – 421,399
Length	163
Max. P	0.906702

overview

Window 4

Location	421,236 – 421,342
Length	106
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	89.37
Mean single sequence MFE	-40.38
Consensus MFE	-31.12
Energy contribution	-31.28
Covariance contribution	0.16
Combinations/Pair	1.13
Mean z-score	-1.51
Structure conservation index	0.77
SVM decision value	0.06
SVM RNA-class probability	0.565363
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 421236 106 - 1281640
---CUGGGUGACCUGACCCUUCAGGGGUUGGUACUACUGCCAAUUGGCUGCGCUUGCGCCUGCGUGGCCCUACACAUGCGUGUAUCUAGAAGCGGGUACACGCAGAAAA
---....(((.(((((....)))))((((((((....))))))))(((..(((........)))..)))...))).(((((((((((......)))))))))))..... ( -46.10)
>DroSec_CAF1 38204 106 - 1
---CUGGGUGACCUGACCCUUCAGGGGUUGGUACUACUGCCAAUUGGCUGCGCUUGCGCGUGCGUUGCCCUACACAUGCGUGUACCUAGCAGCGCCUACACGCAGAAAA
---(((.(((.(((((....)))))((((((((....)))))))).(((((...((((((((.((......)).))))))))......))))).....))).))).... ( -41.90)
>DroSim_CAF1 29718 106 - 1
---CUGGGUGACCUGACCCUUCAGGGGUUGGUACUGCUGCCAAUUGGCUGCGCUUGCGCCUGCGUGGCCCUACACAUGCGUGUACCUAGCAGCGCCUACACGCAGAAAA
---(((.(((....(((((.....)))))((..((((((......(((..(((........)))..))).(((((....)))))..))))))..))..))).))).... ( -45.50)
>DroEre_CAF1 48097 108 - 1
GGGCUGGGUGACCUGACCCUUCAGGGGUUGAUACUGCUGCCAAUUGGCUGCGCUUGCGCCUUCGUGACCCUACACAUGUGUGUAUCUAU-CGUGCGUACACCGAGAAAA
...((.((((.(((((....)))))(((.(((((.((.(((....))).))....((((....(((......)))..))))))))).))-).......)))).)).... ( -33.80)
>DroYak_CAF1 49473 106 - 1
---CUGGGUGACCUGACCCUUCAGGGGUUGAUACUGCUGCCAAUUGGCUGCGCUUGCGCCUGCGUGACCUUACACAUGUGUGUAUCUGUGCUUGCGUACACGUAGAAAA
---..((....)).(((((.....)))))....((((.(((....)))(((((..(((((.....)....(((((....)))))...))))..)))))...)))).... ( -34.60)
>consensus
___CUGGGUGACCUGACCCUUCAGGGGUUGGUACUGCUGCCAAUUGGCUGCGCUUGCGCCUGCGUGGCCCUACACAUGCGUGUAUCUAGCAGCGCGUACACGCAGAAAA
...(((.(((....(((((.....)))))((((((((.(((....))).)))...((((.((.(((....))).)).)))))))))............))).))).... (-31.12 = -31.28 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	421,305 – 421,399
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	92.95
Mean single sequence MFE	-35.25
Consensus MFE	-31.46
Energy contribution	-31.18
Covariance contribution	-0.28
Combinations/Pair	1.08
Mean z-score	-1.45
Structure conservation index	0.89
SVM decision value	1.05
SVM RNA-class probability	0.906702
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 421305 94 - 1281640
UGCCAUCUGGUUCUUUGUCCCCUUAAAACUUGAACGAGGGACUGGACUGGAUUGGGG------CUGGGUGACCUGACCCUUCAGGGGUUGGUACUACUGC
..(((((..((((...((((((.............).))))).))))..)).))).(------(..((((.((.(((((.....)))))))))))...)) ( -33.22)
>DroSec_CAF1 38273 94 - 1
UGCCAUCUGGUUCUUUGUCCCCUUGAAACUUGAACGAGGGACUGGACUAGAUUGGGG------CUGGGUGACCUGACCCUUCAGGGGUUGGUACUACUGC
..(((((((((((...(((((.(((.........)))))))).)))))))).))).(------(..((((.((.(((((.....)))))))))))...)) ( -35.80)
>DroSim_CAF1 29787 94 - 1
UGCCAUCUGGUUCUUUGUCCCCUUGAAACUUGAACGAGGGACUGGACUAGAUUGGGG------CUGGGUGACCUGACCCUUCAGGGGUUGGUACUGCUGC
..(((((((((((...(((((.(((.........)))))))).)))))))).)))((------(.((...(((.(((((.....)))))))).))))).. ( -36.40)
>DroEre_CAF1 48165 100 - 1
UGCCAUCUGGUUCUUUGUCCCCUUGAAACUUGAACGCGGGACUGGACCGGAUUGGGGCUGGGGCUGGGUGACCUGACCCUUCAGGGGUUGAUACUGCUGC
.((((((((((((...((((((.............).))))).)))))))))...))).(((((.((....)).).)))).(((.(((....))).))). ( -39.52)
>DroYak_CAF1 49542 94 - 1
UGCCAUCUGGUUCUUUGUCCCCUUGAAACUUAAAUGAGGAACUGGACCGGAUUGGGG------CUGGGUGACCUGACCCUUCAGGGGUUGAUACUGCUGC
..(((((((((((...((..((((...........)))).)).)))))))).)))((------(.((....)).(((((.....)))))......))).. ( -31.30)
>consensus
UGCCAUCUGGUUCUUUGUCCCCUUGAAACUUGAACGAGGGACUGGACUGGAUUGGGG______CUGGGUGACCUGACCCUUCAGGGGUUGGUACUGCUGC
..(((((((((((...((((((.............).))))).)))))))).)))..........((....)).(((((.....)))))........... (-31.46 = -31.18 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:31 2006