Locus 4821

Sequence ID	2L_DroMel_CAF1
Location	13,744,806 – 13,744,924
Length	118
Max. P	0.953134

overview

Window 1

Location	13,744,806 – 13,744,913
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.66
Mean single sequence MFE	-29.98
Consensus MFE	-26.50
Energy contribution	-27.25
Covariance contribution	0.75
Combinations/Pair	1.08
Mean z-score	-2.21
Structure conservation index	0.88
SVM decision value	1.43
SVM RNA-class probability	0.953134
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13744806 107 + 22407834
---------AA----CACAACUGCUCGAACAGCAAAACUUUUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAAGGACAUAAUUAAUAGUUGGCUAAAAGGUGAGAUAGUCGCACAAAGG
---------..----......((((.....))))...((((((((((((((((.(((((((((((.........)))))))))...(((....)))..)).)))))).)))))).)))). ( -29.70)
>DroSec_CAF1 8387 105 + 1
---------AA------CAACUGCUCGAAUAGCAAAACUUUUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUUGGCUAAAAGGUGAGAUAGUCGCACAAAGG
---------..------....((((.....))))...((((((((((((((((.(((((((((((((.....)))))))))))...(((....)))..)).)))))).)))))).)))). ( -31.10)
>DroAna_CAF1 20322 119 + 1
AACCGGCCAAAAUGCCCAAAAUGCUCGAACAGAAAAACUUUUGCGACAUUCCGACUAUUGUGUCCGUCUAAUGGAGACAUAAUUAAUAGUU-GCCAAAAGGUGAAAUACUCGCACAAAGG
....(((......))).....................(((((((((......(((((((((.(((((...))))).)))......))))))-(((....))).......))))).)))). ( -24.00)
>DroSim_CAF1 10104 105 + 1
---------AA------CAACUGCUCGAAUAGCAAAACUUUUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUUGGCUAAAAGGUGAGAUAGUCGCACAAAGG
---------..------....((((.....))))...((((((((((((((((.(((((((((((((.....)))))))))))...(((....)))..)).)))))).)))))).)))). ( -31.10)
>DroEre_CAF1 10068 110 + 1
---------AAAGGGCCGAAGUGCUCGAACAGCAAAACUUUUGCGACAUUUUGGCUAUUGUGUCCGUCUAGGAUGGACAUAAUUAAUAGUU-GCUAAAAGGUGAGAUAGUCGCACAAAGG
---------...((((......))))...........(((((((((((((((((((((((((((((((...))))))))))....))))))-(((....)))))))).)))))).)))). ( -33.10)
>DroYak_CAF1 10460 110 + 1
---------AAAGGGCCGAACUGCUCGAACAGCAAAACUUUUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUU-GCUAAAAGGUGAGAUAGUCGCACAAAGG
---------...((((......))))...........((((((((((((((((((((((((((((((.....)))))))))....))))))-(((....)))))))).)))))).)))). ( -30.90)
>consensus
_________AA____CCCAACUGCUCGAACAGCAAAACUUUUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUU_GCUAAAAGGUGAGAUAGUCGCACAAAGG
.....................((((.....))))...((((((((((((((((.(((((((((((((.....)))))))))))...(((....)))..)).)))))).)))))).)))). (-26.50 = -27.25 +   0.75)

alignment

secondary structure

dotplot

Window 2

Location	13,744,833 – 13,744,924
Length	91
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.34
Mean single sequence MFE	-27.23
Consensus MFE	-22.47
Energy contribution	-23.05
Covariance contribution	0.58
Combinations/Pair	1.11
Mean z-score	-1.85
Structure conservation index	0.82
SVM decision value	0.54
SVM RNA-class probability	0.774180
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13744833 91 + 22407834
UUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAAGGACAUAAUUAAUAGUUGGCUAAAAGGUGAGAUAGUCGCACAAAGGCCGCA-----------------------------CACAUA
.((((((((((((.(((((((((((.........)))))))))...(((....)))..)).)))))).))))))...........-----------------------------...... ( -24.60)
>DroSec_CAF1 8412 91 + 1
UUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUUGGCUAAAAGGUGAGAUAGUCGCACAAAGGCCGCA-----------------------------CACACA
.((((((((((((.(((((((((((((.....)))))))))))...(((....)))..)).)))))).))))))...........-----------------------------...... ( -26.10)
>DroAna_CAF1 20362 119 + 1
UUGCGACAUUCCGACUAUUGUGUCCGUCUAAUGGAGACAUAAUUAAUAGUU-GCCAAAAGGUGAAAUACUCGCACAAAGGUCGCCAUGUGUGUGCCCCACACCUGGCAUUGUUCCAUGGA
.((.((((....((((.((((((..((((.....))))...........(.-.((....))..).......)))))).))))((((.(((((.....))))).))))..)))).)).... ( -35.70)
>DroSim_CAF1 10129 91 + 1
UUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUUGGCUAAAAGGUGAGAUAGUCGCACAAAGGCCGCA-----------------------------CACACA
.((((((((((((.(((((((((((((.....)))))))))))...(((....)))..)).)))))).))))))...........-----------------------------...... ( -26.10)
>DroEre_CAF1 10099 90 + 1
UUGCGACAUUUUGGCUAUUGUGUCCGUCUAGGAUGGACAUAAUUAAUAGUU-GCUAAAAGGUGAGAUAGUCGCACAAAGGCCGCA-----------------------------CACACA
.((((...(((((((.((((((((((((...))))))))))))........-))))))).((((.....))))........))))-----------------------------...... ( -26.50)
>DroYak_CAF1 10491 90 + 1
UUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUU-GCUAAAAGGUGAGAUAGUCGCACAAAGGCCGCA-----------------------------UACACA
.((((...(((((((.(((((((((((.....)))))))))))........-))))))).((((.....))))........))))-----------------------------...... ( -24.40)
>consensus
UUGCGACAUUUUGGCUAUUGUGUCCGUCUAGCAUGGACAUAAUUAAUAGUU_GCUAAAAGGUGAGAUAGUCGCACAAAGGCCGCA_____________________________CACACA
.((((((((((((.(((((((((((((.....)))))))))))...(((....)))..)).)))))).)))))).............................................. (-22.47 = -23.05 +   0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:18 2006