Locus 1172

Sequence ID	2R_DroMel_CAF1
Location	4,649,722 – 4,649,849
Length	127
Max. P	0.999366

overview

Window 3

Location	4,649,722 – 4,649,820
Length	98
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	89.84
Mean single sequence MFE	-33.70
Consensus MFE	-27.36
Energy contribution	-27.44
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-1.39
Structure conservation index	0.81
SVM decision value	0.08
SVM RNA-class probability	0.575850
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4649722 98 + 20766785
CACACGCAGGGUUGCUUUCCC-GUGAGUUCAAAACAAAGAAGUUAUCGGGCGACAGCACACAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUC
...(((((.(((((((...((-((((.(((........))).)))).(((((...((((.....))))))))).))....))))))).))..))).... ( -32.50)
>DroSec_CAF1 4323 98 + 1
CACACGCAGGGUUGCUUUUCC-GUGAGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACGCAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUC
...(((((.(((((((...((-((((.(((........))).)))).(((((...((((.....))))))))).))....))))))).))..))).... ( -32.50)
>DroSim_CAF1 4386 98 + 1
CACACGCAGGGUUGCUUUUCC-GUGAGUUCAAAACAAAGAAGUUAUCGGGCGAUAGUACGCAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUC
...(((((.(((((((...((-((((.(((........))).)))).(((((...((((.....))))))))).))....))))))).))..))).... ( -30.50)
>DroEre_CAF1 4305 98 + 1
CCUACCCAGGGUUGCUUUUCC-GGGGGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACACACUGUACCGCCCUGGUCGCAGCAGCUGUGGCUGUUAUC
.....(((.(((((((...((-((((.(((........)))((((((....)))))).............))))))....))))))).)))........ ( -32.80)
>DroYak_CAF1 4361 95 + 1
C----CCAGGGUUGCUUUUCCUGGGGGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACACUGUGUGUCGCCCUGGUCGCAGCAGCUGUGGCCGUUAUC
(----((((((.......))))))).......(((............((((((((.(((...))))))))))).((((((((...)))))))))))... ( -40.20)
>consensus
CACACGCAGGGUUGCUUUUCC_GUGAGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACACAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUC
......((.(((((((...((.((((.(((........))).)))).(((((...((((.....))))))))).))....))))))).))......... (-27.36 = -27.44 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	4,649,746 – 4,649,849
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	92.42
Mean single sequence MFE	-32.02
Consensus MFE	-30.08
Energy contribution	-29.48
Covariance contribution	-0.60
Combinations/Pair	1.16
Mean z-score	-1.44
Structure conservation index	0.94
SVM decision value	1.39
SVM RNA-class probability	0.949153
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4649746 103 + 20766785
AGUUCAAAACAAAGAAGUUAUCGGGCGACAGCACACAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUCGGAGCUGCCACUCGAUUUGAAUUUAUAGU
((((((((.(....(((..((((((((...((((.....))))))))).)))))).((((((.(((......))).)))))).....).))))))))...... ( -33.00)
>DroSec_CAF1 4347 103 + 1
AGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACGCAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUCGGAGCUGCCACUCGAUUUGAAUUUGUAAU
((((((((.(....(((..((((((((...((((.....))))))))).)))))).((((((.(((......))).)))))).....).))))))))...... ( -32.30)
>DroSim_CAF1 4410 103 + 1
AGUUCAAAACAAAGAAGUUAUCGGGCGAUAGUACGCAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUCGGAGCUGCCACUCGAUUUGAAUUUGUAAU
((((((((.(....(((..((((((((...((((.....))))))))).)))))).((((((.(((......))).)))))).....).))))))))...... ( -30.30)
>DroEre_CAF1 4329 102 + 1
GGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACACACUGUACCGCCCUGGUCGCAGCAGCUGUGGCUGUUAUCGGAGCUGCCACUCGAUUUGAAUUUA-AAU
((((((((.(......((.((((((((((((......))))..))))).))).)).((((((.(((......))).)))))).....).))))))))..-... ( -30.60)
>DroYak_CAF1 4382 102 + 1
GGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACACUGUGUGUCGCCCUGGUCGCAGCAGCUGUGGCCGUUAUCGGAACUGCCACUCGAUUUGAAUUUG-AAU
.(((((((.((((..(((....((((((((.(((...))))))))))).((((((((...))))))))......((.....)))))...))))..))))-))) ( -33.90)
>consensus
AGUUCAAAACAAAGAAGUUAUCGGGCGAUAGCACACAGUGUGCCGCCCUGGUCUUAGCAGCUGUGACCGUUAUCGGAGCUGCCACUCGAUUUGAAUUUGUAAU
((((((((.(......(..((((((((...((((.....))))))))).)))..).((((((.(((......))).)))))).....).))))))))...... (-30.08 = -29.48 +  -0.60)

alignment

secondary structure

dotplot

Window 5

Location	4,649,746 – 4,649,849
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	92.42
Mean single sequence MFE	-32.66
Consensus MFE	-29.46
Energy contribution	-29.54
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-2.33
Structure conservation index	0.90
SVM decision value	3.54
SVM RNA-class probability	0.999366
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4649746 103 - 20766785
ACUAUAAAUUCAAAUCGAGUGGCAGCUCCGAUAACGGUCACAGCUGCUAAGACCAGGGCGGCACACUGUGUGCUGUCGCCCGAUAACUUCUUUGUUUUGAACU
........((((((.(((((((((((((((....)))....))))))))......(((((((((((...))).)))))))).........)))).)))))).. ( -36.60)
>DroSec_CAF1 4347 103 - 1
AUUACAAAUUCAAAUCGAGUGGCAGCUCCGAUAACGGUCACAGCUGCUAAGACCAGGGCGGCACACUGCGUGCUAUCGCCCGAUAACUUCUUUGUUUUGAACU
........((((((.(((((((((((((((....)))....))))))))......(((((((((.....))))...))))).........)))).)))))).. ( -33.90)
>DroSim_CAF1 4410 103 - 1
AUUACAAAUUCAAAUCGAGUGGCAGCUCCGAUAACGGUCACAGCUGCUAAGACCAGGGCGGCACACUGCGUACUAUCGCCCGAUAACUUCUUUGUUUUGAACU
........((((((.(((((((((((((((....)))....))))))))......(((((((.....)).......))))).........)))).)))))).. ( -28.51)
>DroEre_CAF1 4329 102 - 1
AUU-UAAAUUCAAAUCGAGUGGCAGCUCCGAUAACAGCCACAGCUGCUGCGACCAGGGCGGUACAGUGUGUGCUAUCGCCCGAUAACUUCUUUGUUUUGAACC
...-....((((((.((((..((((((..(........)..))))))..).....((((((((((.....)).))))))))..........))).)))))).. ( -31.60)
>DroYak_CAF1 4382 102 - 1
AUU-CAAAUUCAAAUCGAGUGGCAGUUCCGAUAACGGCCACAGCUGCUGCGACCAGGGCGACACACAGUGUGCUAUCGCCCGAUAACUUCUUUGUUUUGAACC
...-....((((((.((((..(((((((((....)))....))))))..).....(((((((((.....)))...))))))..........))).)))))).. ( -32.70)
>consensus
AUUACAAAUUCAAAUCGAGUGGCAGCUCCGAUAACGGUCACAGCUGCUAAGACCAGGGCGGCACACUGUGUGCUAUCGCCCGAUAACUUCUUUGUUUUGAACU
........((((((.(((((((((((((((....)))....))))))))......(((((((((.....))))...))))).........)))).)))))).. (-29.46 = -29.54 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:15 2006