Locus 6635

Sequence ID	2R_DroMel_CAF1
Location	20,727,003 – 20,727,157
Length	154
Max. P	0.926540

overview

Window 6

Location	20,727,003 – 20,727,117
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	99.65
Mean single sequence MFE	-25.62
Consensus MFE	-25.20
Energy contribution	-25.40
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.98
SVM decision value	0.37
SVM RNA-class probability	0.710681
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20727003 114 - 20766785
GUGCCGUUGGUGAAAAACGAAGAUGAAGAAUGUGUGCACUGAAGCAGGCAUGCAAAAUGUGAGGACUGUCGUUUUUAACAAGGAAAACAAGUUCAUGCGGUAGAAAACACAUAU
....((((.......))))..........((((((...(((..(((.((((.....))))..(((((...((((((......)))))).))))).)))..)))...)))))).. ( -26.00)
>DroSec_CAF1 160608 114 - 1
GUGCCGUUGGUGAAAAACGAAGAUGAAGAAUGUGUGCACUGAAGCAGGCAUGCAAAAUGUGAGGACUGUCGUUUUUAACAAGGAAAACAAGUUCAUGCGGUAGAAAACACAUAU
....((((.......))))..........((((((...(((..(((.((((.....))))..(((((...((((((......)))))).))))).)))..)))...)))))).. ( -26.00)
>DroSim_CAF1 166034 114 - 1
GUGCCGUUGGUGAAAAACGAAGAUGAAGAAUGUGUGCACUGAAGCAGGCAUGCAAAAUGUGAGGACUGUCGUUUUUAACAAGGAAAACAAGUUCAUGCGGUAGAAAACACAUAU
....((((.......))))..........((((((...(((..(((.((((.....))))..(((((...((((((......)))))).))))).)))..)))...)))))).. ( -26.00)
>DroEre_CAF1 201078 114 - 1
GUGCCGUUGGUGAAAAACGAAGAUGAAGAAUGUGUGCAGUGAAGCAGGCAUGCAAAAUGUGAGGACUGUCGUUUUUAACAAGGAAAACAAGUUCAUGCGGUAGAAAACACAUAU
.((((((................((....((((.(((......))).)))).))........(((((...((((((......)))))).)))))..))))))............ ( -24.10)
>DroYak_CAF1 166626 114 - 1
GUGCCGUUGGUGAAAAACGAAGAUGAAGAAUGUGUGCACUGAAGCAGGCAUGCAAAAUGUGAGGACUGUCGUUUUUAACAAGGAAAACAAGUUCAUGCGGUAGAAAACACAUAU
....((((.......))))..........((((((...(((..(((.((((.....))))..(((((...((((((......)))))).))))).)))..)))...)))))).. ( -26.00)
>consensus
GUGCCGUUGGUGAAAAACGAAGAUGAAGAAUGUGUGCACUGAAGCAGGCAUGCAAAAUGUGAGGACUGUCGUUUUUAACAAGGAAAACAAGUUCAUGCGGUAGAAAACACAUAU
....((((.......))))..........((((((...(((..(((.((((.....))))..(((((...((((((......)))))).))))).)))..)))...)))))).. (-25.20 = -25.40 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	20,727,043 – 20,727,157
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	97.72
Mean single sequence MFE	-25.58
Consensus MFE	-24.66
Energy contribution	-24.66
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.96
SVM decision value	1.18
SVM RNA-class probability	0.926540
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20727043 114 + 20766785
AAACGACAGUCCUCACAUUUUGCAUGCCUGCUUCAGUGCACACAUUCUUCAUCUUCGUUUUUCACCAACGGCACCCUGGUCAGAAGGCCGGCAAGAGAUAUUCUGUCCUUCCAU
....(((((........((((((.(((((((......)))................(((.......)))))))...(((((....)))))))))))......)))))....... ( -25.04)
>DroSec_CAF1 160648 114 + 1
AAACGACAGUCCUCACAUUUUGCAUGCCUGCUUCAGUGCACACAUUCUUCAUCUUCGUUUUUCACCAACGGCACCCUGGUCAGAAGGCCUGCAAGAGAUAUUCUGUCCUUCGAU
....(((((........(((((((.((((((......)))..................((((.((((..((...)))))).))))))).)))))))......)))))....... ( -25.64)
>DroSim_CAF1 166074 114 + 1
AAACGACAGUCCUCACAUUUUGCAUGCCUGCUUCAGUGCACACAUUCUUCAUCUUCGUUUUUCACCAACGGCACCCUGGUCAGAAGGCCUGCAAGAGAUAUUCUGUCCUUCGAU
....(((((........(((((((.((((((......)))..................((((.((((..((...)))))).))))))).)))))))......)))))....... ( -25.64)
>DroEre_CAF1 201118 114 + 1
AAACGACAGUCCUCACAUUUUGCAUGCCUGCUUCACUGCACACAUUCUUCAUCUUCGUUUUUCACCAACGGCACCCCGGUCAGAAGGCCGGCAAGAGAUAUUCUGUCCUUCAAU
....(((((........((((((.(((((((......)))................(((.......)))))))...(((((....)))))))))))......)))))....... ( -27.24)
>DroYak_CAF1 166666 114 + 1
AAACGACAGUCCUCACAUUUUGCAUGCCUGCUUCAGUGCACACAUUCUUCAUCUUCGUUUUUCACCAACGGCACCCUGGUCAGAAGGCCGGCAAGAGAUAUCCUGUCCUUCCAU
....(((((........((((((.(((((((......)))................(((.......)))))))...(((((....)))))))))))......)))))....... ( -24.34)
>consensus
AAACGACAGUCCUCACAUUUUGCAUGCCUGCUUCAGUGCACACAUUCUUCAUCUUCGUUUUUCACCAACGGCACCCUGGUCAGAAGGCCGGCAAGAGAUAUUCUGUCCUUCCAU
....(((((........((((((.(((((((......)))................(((.......)))))))....((((....)))).))))))......)))))....... (-24.66 = -24.66 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:48 2006