Locus 1933

Sequence ID	3R_DroMel_CAF1
Location	5,457,438 – 5,457,587
Length	149
Max. P	0.650567

overview

Window 8

Location	5,457,438 – 5,457,553
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.32
Mean single sequence MFE	-35.08
Consensus MFE	-18.62
Energy contribution	-18.68
Covariance contribution	0.06
Combinations/Pair	1.26
Mean z-score	-2.00
Structure conservation index	0.53
SVM decision value	0.24
SVM RNA-class probability	0.650567
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5457438 115 - 27905053
GAACCGGGACUUCUCCUUGUGGAUGACCUCCUUGACUUUCAGGGAGAAUGACUGACCGGGCCAGAGAUCGGCCUGCAGUUCGCUGAACCAUCCGUUGUUAAGGGAAUCCAUUUGU-----
......(((.(((.(((((((((((..(((((((.....)))))))...(((((..((((((.......)))))))))))........))))))....)))))))))))......----- ( -41.60)
>DroPse_CAF1 8663 120 - 1
GUAUUUUGACUUUUCUUUAUGAAUGACAUUUUUUACUUUCAAGGAAAAUGCCUGUCCAGGCCAUAGCUCGGCCUGAAUUUCACUAAACCAGCCGCAAGAUAUCGUAUCCAUUUUAUAUUA
((((((((.......((((((((...((((((((........))))))))......((((((.......))))))...)))).)))).......)))))))).................. ( -22.04)
>DroEre_CAF1 2913 115 - 1
GAACUGGGACUUCUCCUUGUGGAUGACCUCCUUGACUUUCAGGGAGAAGGACUGACCAGGCCAGAGAUCGGCCUGCAGUUCGCUAAACCAUCCGUUGUUAAGGGAAUCCAUUUGU-----
......(((.(((.(((((((((((..(((((((.....)))))))..((((((..((((((.......)))))))))))).......))))))....)))))))))))......----- ( -45.90)
>DroYak_CAF1 2659 115 - 1
AAACUUGGACUUCUCCUUGUGGAUGACCUCCUUGACUUUCAGGGAGAAGGACUGACCAGGCCAGAGAUCGGCCUGCAGUUCGCUGAACCAUCCGUUGUUAAGGGAAUCCAUUUGU-----
.....((((.(((.(((((((((((..(((((((.....)))))))..((((((..((((((.......)))))))))))).......))))))....)))))))))))).....----- ( -46.60)
>DroAna_CAF1 2553 115 - 1
AAACUUUGACUUCUCCUUGUGAAUGACUUCCUUUACUUUCAAGGAGAAGGACUGUCCAGGCCAUAGAUCAGCCUGCAGUUCGCUGAACCAUCCGUUGUUUAGGGAAUCCAUUGGU-----
...(..((.((((((((((.((.(((......))).)).)))))))))).((((..(((((.........)))))))))((.((((((........)))))).))...))..)..----- ( -32.30)
>DroPer_CAF1 7717 120 - 1
GUAUUUUGACUUUUCUUUAUGAAUGACAUUUUUUACUUUCAAGGAAAAUGCCUGUCCAGGCCAUAGCUCGGCCUGAAUUUCACUAAACCAGCCGCAAGAUAUCGUAUCCAUGUUAUAAUA
((((((((.......((((((((...((((((((........))))))))......((((((.......))))))...)))).)))).......)))))))).................. ( -22.04)
>consensus
GAACUUGGACUUCUCCUUGUGAAUGACCUCCUUGACUUUCAAGGAGAAGGACUGACCAGGCCAGAGAUCGGCCUGCAGUUCGCUAAACCAUCCGUUGUUAAGGGAAUCCAUUUGU_____
..........(((((((((.(((.....)))........))))))))).(((((..((((((.......)))))))))))........................................ (-18.62 = -18.68 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	5,457,473 – 5,457,587
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.27
Mean single sequence MFE	-31.36
Consensus MFE	-20.38
Energy contribution	-20.30
Covariance contribution	-0.08
Combinations/Pair	1.31
Mean z-score	-1.50
Structure conservation index	0.65
SVM decision value	0.19
SVM RNA-class probability	0.624374
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5457473 114 - 27905053
------AUUUAUCUUACGUUUCAACGAUCUGGAUGUCUUGGAACCGGGACUUCUCCUUGUGGAUGACCUCCUUGACUUUCAGGGAGAAUGACUGACCGGGCCAGAGAUCGGCCUGCAGUU
------..((((((..(((....)))....(((.((((((....))))))...)))....)))))).(((((((.....)))))))...(((((..((((((.......))))))))))) ( -38.50)
>DroPse_CAF1 8703 120 - 1
ACAUAUGUAUAACUCACGUUUCAAUUAUUUGAAUAUCUUGGUAUUUUGACUUUUCUUUAUGAAUGACAUUUUUUACUUUCAAGGAAAAUGCCUGUCCAGGCCAUAGCUCGGCCUGAAUUU
...................(((((....)))))......((((((((..(((........(((......)))........))).))))))))....((((((.......))))))..... ( -20.69)
>DroEre_CAF1 2948 114 - 1
------AUUUAUCUUACGUUUCAACGAUCUGGAUGUCCUGGAACUGGGACUUCUCCUUGUGGAUGACCUCCUUGACUUUCAGGGAGAAGGACUGACCAGGCCAGAGAUCGGCCUGCAGUU
------......(((.....(((.(.((..(((.(((((......)))))...)))..)).).))).(((((((.....))))))))))(((((..((((((.......))))))))))) ( -38.90)
>DroYak_CAF1 2694 114 - 1
------AUUUAUCUUACGUUUCAACGAUCUGGAUGUCCUGAAACUUGGACUUCUCCUUGUGGAUGACCUCCUUGACUUUCAGGGAGAAGGACUGACCAGGCCAGAGAUCGGCCUGCAGUU
------......(((.....(((.(.((..(((.((((........))))...)))..)).).))).(((((((.....))))))))))(((((..((((((.......))))))))))) ( -37.90)
>DroAna_CAF1 2588 114 - 1
------AUUAGACUUACGUUUCGACGAUUUGAAUGUCCUGAAACUUUGACUUCUCCUUGUGAAUGACUUCCUUUACUUUCAAGGAGAAGGACUGUCCAGGCCAUAGAUCAGCCUGCAGUU
------...........((((((..(((......))).)))))).....((((((((((.((.(((......))).)).))))))))))(((((..(((((.........)))))))))) ( -31.50)
>DroPer_CAF1 7757 120 - 1
ACAUAUGUAUAACUCACGUUUCAAUUAUUUGAAUAUCUUGGUAUUUUGACUUUUCUUUAUGAAUGACAUUUUUUACUUUCAAGGAAAAUGCCUGUCCAGGCCAUAGCUCGGCCUGAAUUU
...................(((((....)))))......((((((((..(((........(((......)))........))).))))))))....((((((.......))))))..... ( -20.69)
>consensus
______AUUUAACUUACGUUUCAACGAUCUGAAUGUCCUGGAACUUGGACUUCUCCUUGUGAAUGACCUCCUUGACUUUCAAGGAGAAGGACUGACCAGGCCAGAGAUCGGCCUGCAGUU
.................((((((..(((......))).))))))......(((((((((.(((.....)))........))))))))).(((((..((((((.......))))))))))) (-20.38 = -20.30 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:14 2006