Locus 5879

Sequence ID	3L_DroMel_CAF1
Location	15,821,464 – 15,821,578
Length	114
Max. P	0.922969

overview

Window 2

Location	15,821,464 – 15,821,578
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	95.26
Mean single sequence MFE	-58.43
Consensus MFE	-56.45
Energy contribution	-56.85
Covariance contribution	0.40
Combinations/Pair	1.05
Mean z-score	-1.31
Structure conservation index	0.97
SVM decision value	1.15
SVM RNA-class probability	0.922969
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15821464 114 + 23771897
AACGCAUGCCGCCGCCGAAGAACUCCUCCGGAUCGGUGAUCCUUGGGGUACCGGGCGUGGCCACCGAGGAUGAGGCGGCCGGGGUACCACUGGACAUGGGCGUGGCCCCGCCCA
...((..(((((((((((.....(((...)))))))).(((((((((((..(....)..))).))))))))..)))))).(((((.(((.......))).....)))))))... ( -49.70)
>DroSec_CAF1 28889 114 + 1
AACGCAUGCCGCCGCCGAAGAACUCCUCCGGAUCGGUGGUCCUUGGGGUGCCGGGCGUGGCCACCGAGGAGGAGGCGGCCGGGGUGCCACUGGACAUGGGCGUGGCACCGCCCA
...((((.((((((((.......((((((...((((((((((((((....)))))...)))))))))))))))))))).))).)))).........((((((......)))))) ( -60.91)
>DroSim_CAF1 29472 114 + 1
AACGCAUGCCGCCGCCGAAGAACUCCUCCGGAUCGGUGGUCCUUGGGGUGCCGGGCGUGGCCACCGAGGAGGAGGCGGCCGGGGUGCCACUGGACAUGGGCGUGGCACCGCCCA
...((((.((((((((.......((((((...((((((((((((((....)))))...)))))))))))))))))))).))).)))).........((((((......)))))) ( -60.91)
>DroEre_CAF1 27798 114 + 1
AACGCAUGCCGCCGCCAAAGAACUCCUCCGGAUCGGUGGUCCUUGGGGUUCCAGGCGUGGCCACCGAGGAGGAGGCGGCCGGGGUGCCACUGGACAUGGGCGUGGCACCGCCCA
...((((.((((((((.......((((((...((((((((((((((....)))))...)))))))))))))))))))).))).)))).........((((((......)))))) ( -61.51)
>DroYak_CAF1 70071 114 + 1
AGCGCAUACCGCCGCCGAAGAACUCCUCUGGAUCGGUGGUCCUUGGGGUUCCAGGUGUCGCCACCGAGGAGGAGGCGGCCGGGGUGCCACUGGACAUGGGCGUGGCACCGCCCA
.(.((...((((((((......((((((.((...(((((..(((((....)))))..))))).))))))))..))))).)))((((((((...........)))))))))).). ( -59.10)
>consensus
AACGCAUGCCGCCGCCGAAGAACUCCUCCGGAUCGGUGGUCCUUGGGGUGCCGGGCGUGGCCACCGAGGAGGAGGCGGCCGGGGUGCCACUGGACAUGGGCGUGGCACCGCCCA
...((((.((((((((.......((((((...((((((((((((((....)))))...)))))))))))))))))))).))).)))).........((((((......)))))) (-56.45 = -56.85 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	15,821,464 – 15,821,578
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	95.26
Mean single sequence MFE	-55.34
Consensus MFE	-51.00
Energy contribution	-51.32
Covariance contribution	0.32
Combinations/Pair	1.09
Mean z-score	-1.39
Structure conservation index	0.92
SVM decision value	1.06
SVM RNA-class probability	0.909171
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15821464 114 - 23771897
UGGGCGGGGCCACGCCCAUGUCCAGUGGUACCCCGGCCGCCUCAUCCUCGGUGGCCACGCCCGGUACCCCAAGGAUCACCGAUCCGGAGGAGUUCUUCGGCGGCGGCAUGCGUU
.((((((((((((...........))))..))))(((((((........)))))))..))))(.(.((((..(((((...))))).((((....)))))).)).).)....... ( -50.50)
>DroSec_CAF1 28889 114 - 1
UGGGCGGUGCCACGCCCAUGUCCAGUGGCACCCCGGCCGCCUCCUCCUCGGUGGCCACGCCCGGCACCCCAAGGACCACCGAUCCGGAGGAGUUCUUCGGCGGCGGCAUGCGUU
..((.((((((((...........)))))))))).(((((((((((((((((((((......))).((....))..))))))...))))))...(....).))))))....... ( -57.20)
>DroSim_CAF1 29472 114 - 1
UGGGCGGUGCCACGCCCAUGUCCAGUGGCACCCCGGCCGCCUCCUCCUCGGUGGCCACGCCCGGCACCCCAAGGACCACCGAUCCGGAGGAGUUCUUCGGCGGCGGCAUGCGUU
..((.((((((((...........)))))))))).(((((((((((((((((((((......))).((....))..))))))...))))))...(....).))))))....... ( -57.20)
>DroEre_CAF1 27798 114 - 1
UGGGCGGUGCCACGCCCAUGUCCAGUGGCACCCCGGCCGCCUCCUCCUCGGUGGCCACGCCUGGAACCCCAAGGACCACCGAUCCGGAGGAGUUCUUUGGCGGCGGCAUGCGUU
..((.((((((((...........)))))))))).(((((((((((((((((((.....(((((....)).))).)))))))...))))))((......))))))))....... ( -58.60)
>DroYak_CAF1 70071 114 - 1
UGGGCGGUGCCACGCCCAUGUCCAGUGGCACCCCGGCCGCCUCCUCCUCGGUGGCGACACCUGGAACCCCAAGGACCACCGAUCCAGAGGAGUUCUUCGGCGGCGGUAUGCGCU
.(.((((((((((...........))))))))(((.((((((((((.(((((((.....(((((....)).))).)))))))....)))))(.....)))))))))...)).). ( -53.20)
>consensus
UGGGCGGUGCCACGCCCAUGUCCAGUGGCACCCCGGCCGCCUCCUCCUCGGUGGCCACGCCCGGAACCCCAAGGACCACCGAUCCGGAGGAGUUCUUCGGCGGCGGCAUGCGUU
..((.((((((((...........)))))))))).(((((((((((((((((((((......((....))..)).)))))))...))))))((......))))))))....... (-51.00 = -51.32 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:46 2006