Locus 4659

Sequence ID	2L_DroMel_CAF1
Location	13,354,669 – 13,354,774
Length	105
Max. P	0.915479

overview

Window 7

Location	13,354,669 – 13,354,774
Length	105
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	83.71
Mean single sequence MFE	-36.12
Consensus MFE	-20.92
Energy contribution	-21.96
Covariance contribution	1.04
Combinations/Pair	1.14
Mean z-score	-2.87
Structure conservation index	0.58
SVM decision value	1.10
SVM RNA-class probability	0.915479
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13354669 105 + 22407834
UGGAGAG------CGGCUCUUUUCAGAGAGCGGAAAGGAAAAGCCGUGAGCAAACGGAGAUUGCGCUCUCAGGACACUUUUCCUUGCUGGCCAAUUGGAAAGGAAAAAUCA
..(((((------((((((((....))))))............((((......))))......))))))).......((((((((.....((....)).)))))))).... ( -35.40)
>DroSec_CAF1 66839 105 + 1
UGGAGAG------CGGCUCUUUUCAGAGAGCGGAAAGGAAAAGCCGUGAGCAAACGGAGAUUGCGCUCUCAGGACACUUUUCCUUGCUGGCCAAUUGGAAAGGAAAAAUCA
..(((((------((((((((....))))))............((((......))))......))))))).......((((((((.....((....)).)))))))).... ( -35.40)
>DroSim_CAF1 69594 105 + 1
UGGAGAG------CGGCUCUUUUCAGAGAGCGGAAAGGAAAAGCCGUGAGCAAACGGAGAUUGCGCUCUCAGGACACUUUUCCUUGCUGGCCAAUUGGAAAGGAAAAAUCA
..(((((------((((((((....))))))............((((......))))......))))))).......((((((((.....((....)).)))))))).... ( -35.40)
>DroYak_CAF1 68614 105 + 1
UGGAGAG------CGGCUCCUUUCAGAGAGCGAAAAGGAAAAGCCGUGAGCAAACGGAGAUUGCGCUCUCAGGCCACUUUUCCUUGCUGGCCAAUUGGAAAGGAAAAAUCA
....((.------....(((((((.(((((((...((......((((......))))...)).))))))).((((((........).))))).....)))))))....)). ( -36.60)
>DroAna_CAF1 74351 110 + 1
GAGAGAGAGAGAGCAGGG-AUUUGAGAAAACGGCUCGAAAGAGCGCAGGAGAGAGUACUAUCUCUCUCGCAGGACACUUUUCCUUGCUGGCCAAUUAUUGAGGAAAAAUCA
......(.(..(((((((-(...(((......((((....))))((..((((((......))))))..))......))).))))))))..))................... ( -37.80)
>consensus
UGGAGAG______CGGCUCUUUUCAGAGAGCGGAAAGGAAAAGCCGUGAGCAAACGGAGAUUGCGCUCUCAGGACACUUUUCCUUGCUGGCCAAUUGGAAAGGAAAAAUCA
..(((((........((((((....)))))).....(.((...((((......))))...)).).))))).......((((((((.((........)).)))))))).... (-20.92 = -21.96 +   1.04)

alignment

secondary structure

dotplot

Window 8

Location	13,354,669 – 13,354,774
Length	105
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	83.71
Mean single sequence MFE	-30.07
Consensus MFE	-16.96
Energy contribution	-17.36
Covariance contribution	0.40
Combinations/Pair	1.28
Mean z-score	-2.28
Structure conservation index	0.56
SVM decision value	0.23
SVM RNA-class probability	0.646241
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13354669 105 - 22407834
UGAUUUUUCCUUUCCAAUUGGCCAGCAAGGAAAAGUGUCCUGAGAGCGCAAUCUCCGUUUGCUCACGGCUUUUCCUUUCCGCUCUCUGAAAAGAGCCG------CUCUCCA
..((((((((((.((....)).....)))))))))).....((((((((((.......))))....(((((((...(((........)))))))))))------))))).. ( -30.40)
>DroSec_CAF1 66839 105 - 1
UGAUUUUUCCUUUCCAAUUGGCCAGCAAGGAAAAGUGUCCUGAGAGCGCAAUCUCCGUUUGCUCACGGCUUUUCCUUUCCGCUCUCUGAAAAGAGCCG------CUCUCCA
..((((((((((.((....)).....)))))))))).....((((((((((.......))))....(((((((...(((........)))))))))))------))))).. ( -30.40)
>DroSim_CAF1 69594 105 - 1
UGAUUUUUCCUUUCCAAUUGGCCAGCAAGGAAAAGUGUCCUGAGAGCGCAAUCUCCGUUUGCUCACGGCUUUUCCUUUCCGCUCUCUGAAAAGAGCCG------CUCUCCA
..((((((((((.((....)).....)))))))))).....((((((((((.......))))....(((((((...(((........)))))))))))------))))).. ( -30.40)
>DroYak_CAF1 68614 105 - 1
UGAUUUUUCCUUUCCAAUUGGCCAGCAAGGAAAAGUGGCCUGAGAGCGCAAUCUCCGUUUGCUCACGGCUUUUCCUUUUCGCUCUCUGAAAGGAGCCG------CUCUCCA
..((((((((((.((....)).....)))))))))).....((((((((((.......))))....(((...(((((((........)))))))))))------))))).. ( -32.80)
>DroAna_CAF1 74351 110 - 1
UGAUUUUUCCUCAAUAAUUGGCCAGCAAGGAAAAGUGUCCUGCGAGAGAGAUAGUACUCUCUCCUGCGCUCUUUCGAGCCGUUUUCUCAAAU-CCCUGCUCUCUCUCUCUC
........................(((.(((......))))))((((((((.((((.........((((((....))).)))..........-...)))).)))))))).. ( -26.35)
>consensus
UGAUUUUUCCUUUCCAAUUGGCCAGCAAGGAAAAGUGUCCUGAGAGCGCAAUCUCCGUUUGCUCACGGCUUUUCCUUUCCGCUCUCUGAAAAGAGCCG______CUCUCCA
...................(((.(((((((((((((.....((((......))))((........))))))))))))...))).(((....)))))).............. (-16.96 = -17.36 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:56 2006