Locus 3412

Sequence ID	3R_DroMel_CAF1
Location	9,250,886 – 9,251,056
Length	170
Max. P	0.782509

overview

Window 5

Location	9,250,886 – 9,251,002
Length	116
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	91.72
Mean single sequence MFE	-22.98
Consensus MFE	-19.45
Energy contribution	-20.43
Covariance contribution	0.99
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.85
SVM decision value	0.13
SVM RNA-class probability	0.597973
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9250886 116 + 27905053
AUUUCCAUCGCAACCAUGUAUGGAUUGGGCCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACACGCCACCCAUACAUCUGCAGACACCUCCGCAGCUGCAGA
................(((((((....(((((((((....))))))...........(......).............)))..)))))))(((((((.(.........)))))))) ( -25.30)
>DroSec_CAF1 21758 116 + 1
AUUUCCAUCGCAACCAUGUAUGGAUUGGGCCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACACGCCACCCAUACAUCUGCAGACACCUCCGCAGCUGCAGA
................(((((((....(((((((((....))))))...........(......).............)))..)))))))(((((((.(.........)))))))) ( -25.30)
>DroSim_CAF1 21834 116 + 1
AUUUCCAUCGCAACCAUGUAUGGAUUGGGCCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACACGCCACCCAUACAUCUGCAGACACCUCCGCAGCUGCAGA
................(((((((....(((((((((....))))))...........(......).............)))..)))))))(((((((.(.........)))))))) ( -25.30)
>DroEre_CAF1 22148 116 + 1
AUUUCCAUCGCAACCAUGUAUGGAUUGGGCCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACAUGCCACCCAUACAUCUGCAGAUACCUCCGCAGCUGCAGA
.........(((...((((((((....(((((((((....))))))...........(......).............)))..))))))))((((.((....)).)))).)))... ( -25.00)
>DroYak_CAF1 21611 116 + 1
AUUUCCAUCGCAACCAUGUAUGGAUUGGGCCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACAUGCCACCCAUACAUCUGCAGAUACCUCCGCAGCUGCAGA
.........(((...((((((((....(((((((((....))))))...........(......).............)))..))))))))((((.((....)).)))).)))... ( -25.00)
>DroAna_CAF1 21522 94 + 1
AUUUCCAUCGCAACCAUGUAUGGAUUGGACCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACACGGCACUCAUACU----------------------CAGA
...(((((.(((....))))))))..........((((...((((............))))..........((....)))))).......----------------------.... ( -12.00)
>consensus
AUUUCCAUCGCAACCAUGUAUGGAUUGGGCCAACGUGCAAAUGUUGAUUAAAAAUUAGACAAAACAAAAAACGAACACGCCACCCAUACAUCUGCAGACACCUCCGCAGCUGCAGA
................(((((((....(((((((((....))))))...........(......).............)))..)))))))(((((((............))))))) (-19.45 = -20.43 +   0.99)

alignment

secondary structure

dotplot

Window 6

Location	9,250,962 – 9,251,056
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	88.90
Mean single sequence MFE	-28.42
Consensus MFE	-21.24
Energy contribution	-22.28
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.93
Structure conservation index	0.75
SVM decision value	0.56
SVM RNA-class probability	0.782509
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9250962 94 - 27905053
UCCGAAUCCGAAUCGUUAUCUUUAUAUGUAUU------UGUAUCUGUUGCUAUAUCUUUGUCUGCAGCUGCGGAGGUGUCUGCAGAUGUAUGGGUGGCGU
.............((((((((.(((((.....------.......(((((.(((....)))..)))))((((((....)))))).))))).)))))))). ( -23.20)
>DroSec_CAF1 21834 100 - 1
UCCGAAUCCGAAUCGUUUUCUGUAUCUGUAUUUGUAUUUGUAUCUGUUGCUGUAUCUUUGUCUGCAGCUGCGGAGGUGUCUGCAGAUGUAUGGGUGGCGU
.............(((..(((((((....(((((((..((..(((((.((((((........)))))).)))))..))..))))))))))))))..))). ( -26.80)
>DroSim_CAF1 21910 100 - 1
UCCGAAUCCGAAUCGUUAUCUGUAUUUGUAUUUGUAUUUGAAUUUGUAUCUGUAUCUUUGUCUGCAGCUGCGGAGGUGUCUGCAGAUGUAUGGGUGGCGU
.............((((((((((((....(((((((..((..((((((.(((((........))))).))))))..))..))))))))))))))))))). ( -25.90)
>DroEre_CAF1 22224 94 - 1
UCCGAAUCCGUAUCUUCAUCUGUAUUUGUACC------UGUAUCUGUAGCUGUAUCUUUGUCUGCAGCUGCGGAGGUAUCUGCAGAUGUAUGGGUGGCAU
...(.(((((((....((((((((...(((((------....((((((((((((........))))))))))))))))).)))))))))))))))..).. ( -37.60)
>DroYak_CAF1 21687 94 - 1
UCCGAAUCCGAAUCGUUAUCUGUAUUUGUAUU------UGUAUCUGUAGCGGUAUCUUUGUCUGCAGCUGCGGAGGUAUCUGCAGAUGUAUGGGUGGCAU
..............((((((((((((((((..------((..((((((((.(((........))).))))))))..))..)))))..))))))))))).. ( -28.60)
>consensus
UCCGAAUCCGAAUCGUUAUCUGUAUUUGUAUU______UGUAUCUGUAGCUGUAUCUUUGUCUGCAGCUGCGGAGGUGUCUGCAGAUGUAUGGGUGGCGU
..............(((((((((((.................((((((((((((........))))))))))))...(((....)))))))))))))).. (-21.24 = -22.28 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:21 2006