Locus 741

Sequence ID	3L_DroMel_CAF1
Location	2,229,665 – 2,229,825
Length	160
Max. P	0.909925

overview

Window 3

Location	2,229,665 – 2,229,785
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.58
Mean single sequence MFE	-38.06
Consensus MFE	-29.66
Energy contribution	-30.06
Covariance contribution	0.40
Combinations/Pair	1.12
Mean z-score	-2.07
Structure conservation index	0.78
SVM decision value	1.07
SVM RNA-class probability	0.909925
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2229665 120 + 23771897
AGGAGGGUACUGAUACGGCCAAGCUGGAUCCUCUCCUGCAGCGGUCUAAUCUGAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACACCGACGACUUGGAGGACGAUAAUU
(((.((((((((((..((((..((.(((.....))).))...))))..)))..))))))).)))........((((((((((((.(((((.(....)))).)).)))))))))))).... ( -43.50)
>DroSec_CAF1 10595 120 + 1
AGAAGGGUACUGAUACGGCCAAGCUAGAUCCUCUCCUGCAGCGAUCUAAUCUAAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACGCCGAUGACUUGGAGGACGACAAUU
....((((((((((..(((...)))((((((((....).)).))))).)))..)))))))............((((((((((((...(((.......)))....)))))))))))).... ( -36.70)
>DroSim_CAF1 10684 120 + 1
AGAAGGGUACUGAUACGGCCAAGCUAGAUCCUCUCCUGCAGCGAUCUAAUCUAAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACGCCGAUGACUUGGAGGACGACAAUU
....((((((((((..(((...)))((((((((....).)).))))).)))..)))))))............((((((((((((...(((.......)))....)))))))))))).... ( -36.70)
>DroEre_CAF1 23620 119 + 1
AGGAGGGUACCGAAACGGCCAAGCAAGAUCC-CUCCUGCAACGGUCUAAUCUGAGUACCUACCUGAUAAGAAGUCGACUUCCAAACUUCGAGGACACCGAUGACUUGGAGGACGACAAUA
(((.(((((((((...((((..(((.((...-.)).)))...))))...)).).)))))).)))........((((.(((((((...(((.(....))))....))))))).)))).... ( -37.10)
>DroYak_CAF1 11117 120 + 1
AGGAGGGUACCGAGACGGCCAAACAGGAUCCUCUCCUGCAACGUUCUAAUCUAAGUACCUACCUAAUAAGAAGUCGACUUCCAAAUUUCGAGGACUCCGAUGACUUGGAGGACGACAAUA
(((.((((((..(((.(((....(((((.....)))))....)))....)))..)))))).)))........((((.(((((((...(((.......)))....))))))).)))).... ( -36.30)
>consensus
AGGAGGGUACUGAUACGGCCAAGCUAGAUCCUCUCCUGCAGCGAUCUAAUCUAAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACACCGAUGACUUGGAGGACGACAAUU
(((.((((((.......((...)).(((((............))))).......)))))).)))........((((((((((((...(((.(....))))....)))))))))))).... (-29.66 = -30.06 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	2,229,705 – 2,229,825
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-32.24
Consensus MFE	-27.50
Energy contribution	-27.74
Covariance contribution	0.24
Combinations/Pair	1.18
Mean z-score	-1.47
Structure conservation index	0.85
SVM decision value	0.53
SVM RNA-class probability	0.771019
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2229705 120 + 23771897
GCGGUCUAAUCUGAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACACCGACGACUUGGAGGACGAUAAUUUCUCGCUGAACGACUACCGUUUCAGCUUCAGUUUCAGUCA
..(((((......)).)))...((((...(((((((((((((((.(((((.(....)))).)).))))))))))))........((((((((.....)).)))))))))....))))... ( -35.80)
>DroSec_CAF1 10635 120 + 1
GCGAUCUAAUCUAAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACGCCGAUGACUUGGAGGACGACAAUUUCUCGCUGAACGACUAUCGUUUCAGCUUCAGUUUUAGUGA
.................((((.((((......((((((((((((...(((.......)))....))))))))))))........((((((((.....)).)))))).))))...))).). ( -34.70)
>DroSim_CAF1 10724 120 + 1
GCGAUCUAAUCUAAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACGCCGAUGACUUGGAGGACGACAAUUUCCCGCUGAACGACUAUCGUUUCAGCUUCAGUUUCAGUGA
.....................(((((...(((((((((((((((...(((.......)))....))))))))))))........((((((((.....)).)))))))))....)))).). ( -35.40)
>DroEre_CAF1 23659 120 + 1
ACGGUCUAAUCUGAGUACCUACCUGAUAAGAAGUCGACUUCCAAACUUCGAGGACACCGAUGACUUGGAGGACGACAAUAUCUCGCUGAACGACUACCGUUUCAGCUUUAGUUUCAGUCA
..(((((......)).)))...((((......((((.(((((((...(((.(....))))....))))))).))))........((((((((.....)).)))))).......))))... ( -32.40)
>DroYak_CAF1 11157 120 + 1
ACGUUCUAAUCUAAGUACCUACCUAAUAAGAAGUCGACUUCCAAAUUUCGAGGACUCCGAUGACUUGGAGGACGACAAUAUCUCGCAGAACGACUACAACUUCAGUUUUAUUUUCACCCA
.((((((..(((...((......))...))).((((.(((((((...(((.......)))....))))))).))))..........))))))............................ ( -22.90)
>consensus
GCGAUCUAAUCUAAGUACCUACCUGAUAAGAAGUCGUCUUCCGAAUUUCGAGGACACCGAUGACUUGGAGGACGACAAUUUCUCGCUGAACGACUACCGUUUCAGCUUCAGUUUCAGUCA
......................((((......((((((((((((...(((.(....))))....))))))))))))........((((((((.....)).)))))).))))......... (-27.50 = -27.74 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:55 2006