Locus 613

Sequence ID	2L_DroMel_CAF1
Location	1,825,401 – 1,825,561
Length	160
Max. P	0.992370

overview

Window 3

Location	1,825,401 – 1,825,521
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.00
Mean single sequence MFE	-42.43
Consensus MFE	-35.32
Energy contribution	-34.44
Covariance contribution	-0.88
Combinations/Pair	1.31
Mean z-score	-2.40
Structure conservation index	0.83
SVM decision value	2.32
SVM RNA-class probability	0.992370
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1825401 120 - 22407834
AUUAGCCAAAAACGAGGGUUGCUUCGAUAAUAAGUUCUGUUCCGAGCAGCCAAAAUGUACGGGCGGAGUUCAUGAUUGUCGCUUUGUGGAGUCGAACAUGAAGAUUUGUCAGGCGGAAAA
....(((.........((((((((.((.............)).))))))))..........((((((.((((((....((((((....))).))).))))))..)))))).)))...... ( -33.62)
>DroSec_CAF1 45462 120 - 1
CUCCGCCAAAAACGAGGGUUGCUUCGACAAUAAGUUUUGUUCCGAGCAACCAAAGUGUACGGGCGGAGUUCACGAUUGUCGCUUUGUGGAGUCAAGUAUGCAGAUUUGUCAGGCGGAAAA
.((((((....(((((((((((((.(((((......))).)).))))))))...((((((.....((.(((((((........))))))).))..))))))...)))))..))))))... ( -44.00)
>DroSim_CAF1 23171 120 - 1
CUCCGCCAAAAACGAGGGUUGCUUCGAUAAUAAGUUCUGUUCCGAGCAACCAAAGUGUACGGGCGGAGUUCACGAUUGUCGCUUUGUGGAGUCAAGUAUGCAGAUUUGCCAGGCGGAAAA
.((((((.........((((((((.((.............)).))))))))...((((((.....((.(((((((........))))))).))..))))))..........))))))... ( -40.72)
>DroEre_CAF1 33935 120 - 1
AUCCGCCAGAAAUGAGGGCUGCUUCGAUAGUGAGUUCUGUUCCGAGCAGCCCAAGUGUUCGGGAGGAGUGCACGAUUGCCGCUUUGUGGAGUCGAAUAUGCAGAUUUGCCAGGCGGAAAA
.((((((.(((((..(((((((((.(((((......))).)).)))))))))..)).)))((.(((..(((((((((.((((...)))))))))....))))..))).)).))))))... ( -50.20)
>DroYak_CAF1 10328 120 - 1
GUCCGCCAGAAAUGAGGGCUGUUUCGAUAGUAAGUUCUGUUCCGAGCAGCCAAAAUGUUCGGGCGGAGUGCACGAUUGCCGCUUUGUGGAGUCGUCUAUGAAGAUUUGUCAGGCGGAAAA
.((((((.(((((.......)))))(((((((...(((((.(((((((.......)))))))))))).)))((((((.((((...))))))))))...........)))).))))))... ( -43.60)
>consensus
AUCCGCCAAAAACGAGGGUUGCUUCGAUAAUAAGUUCUGUUCCGAGCAGCCAAAGUGUACGGGCGGAGUUCACGAUUGUCGCUUUGUGGAGUCGAAUAUGCAGAUUUGUCAGGCGGAAAA
.((((((....((...((((((((.(((((......))).)).))))))))...)).....))))))...........((((((.(..((.((.........))))..).)))))).... (-35.32 = -34.44 +  -0.88)

alignment

secondary structure

dotplot

Window 4

Location	1,825,441 – 1,825,561
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.92
Mean single sequence MFE	-42.04
Consensus MFE	-32.18
Energy contribution	-31.90
Covariance contribution	-0.28
Combinations/Pair	1.31
Mean z-score	-2.09
Structure conservation index	0.77
SVM decision value	0.98
SVM RNA-class probability	0.894679
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1825441 120 - 22407834
ACAGCGAUGGAGCGUGCAAUCAGGAAUGUGGUUACUACAAAUUAGCCAAAAACGAGGGUUGCUUCGAUAAUAAGUUCUGUUCCGAGCAGCCAAAAUGUACGGGCGGAGUUCAUGAUUGUC
...((......))..(((((((.((((.((((((........))))))....(((((....))))).........(((((.(((.(((.......))).)))))))))))).))))))). ( -32.90)
>DroSec_CAF1 45502 120 - 1
AUAGCGAUGGAGCCUGCAAUCAUGACUGUGGCUACUACAACUCCGCCAAAAACGAGGGUUGCUUCGACAAUAAGUUUUGUUCCGAGCAACCAAAGUGUACGGGCGGAGUUCACGAUUGUC
...(((((.(((((.(((........))))))).....(((((((((....((...((((((((.(((((......))).)).))))))))...)).....)))))))))..).))))). ( -45.30)
>DroSim_CAF1 23211 120 - 1
AUAGCGAUGGAGCCUGCAAUCAUGACUGUGGCUACUACAACUCCGCCAAAAACGAGGGUUGCUUCGAUAAUAAGUUCUGUUCCGAGCAACCAAAGUGUACGGGCGGAGUUCACGAUUGUC
...(((((.(((((.(((........))))))).....(((((((((....((...((((((((.((.............)).))))))))...)).....)))))))))..).))))). ( -42.52)
>DroEre_CAF1 33975 120 - 1
ACGACGAUGGAACGUGCCGCCGAGACUGUGGCUACUACAAAUCCGCCAGAAAUGAGGGCUGCUUCGAUAGUGAGUUCUGUUCCGAGCAGCCCAAGUGUUCGGGAGGAGUGCACGAUUGCC
............((((((((((......)))).........(((.((.(((((..(((((((((.(((((......))).)).)))))))))..)).))).)).)))).)))))...... ( -42.20)
>DroYak_CAF1 10368 120 - 1
ACAGCGAUGGAGUGUGCAGUCGAGAUUGCGGCUACUACAAGUCCGCCAGAAAUGAGGGCUGUUUCGAUAGUAAGUUCUGUUCCGAGCAGCCAAAAUGUUCGGGCGGAGUGCACGAUUGCC
...(((((...(((..((((((......)))))........((((((.(((.....((((((((.(((((......))).)).))))))))......))).)))))))..))).))))). ( -47.30)
>consensus
ACAGCGAUGGAGCGUGCAAUCAAGACUGUGGCUACUACAAAUCCGCCAAAAACGAGGGUUGCUUCGAUAAUAAGUUCUGUUCCGAGCAGCCAAAGUGUACGGGCGGAGUUCACGAUUGUC
...............((((((.....(((((...)))))..((((((....((...((((((((.(((((......))).)).))))))))...)).....))))))......)))))). (-32.18 = -31.90 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:59 2006