Locus 1610

Sequence ID	2L_DroMel_CAF1
Location	4,333,676 – 4,333,776
Length	100
Max. P	0.792627

overview

Window 5

Location	4,333,676 – 4,333,776
Length	100
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	74.70
Mean single sequence MFE	-29.38
Consensus MFE	-19.52
Energy contribution	-21.08
Covariance contribution	1.56
Combinations/Pair	1.05
Mean z-score	-1.55
Structure conservation index	0.66
SVM decision value	0.59
SVM RNA-class probability	0.792627
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4333676 100 + 22407834
UAUCUGAAAGAUGCGUUAACUAUUAUUUAUAAUUUGUAUCCGAGAGUCAGGUACAA--GCAGCCAGGCAGCACUAUUGCUAUCCGGAUGGCUGCGCUGGCUC
(((((((..((((((...................))))))(....))))))))...--..(((((((((((.(.(((........))))))))).)))))). ( -27.81)
>DroSec_CAF1 2647 100 + 1
UAUCUGAAAGAUGCCUUAACUAUUAUUUAUAAUUUGUAUCCGAGAGUCAGGUACAA--GCAGCCAGGCAGCACUGACACUAUCCGGAUGGCUGCGCUGGCUC
(((((((..(((((...((.(((.....))).)).)))))(....))))))))...--..(((((((((((.(((........)))...))))).)))))). ( -29.50)
>DroSim_CAF1 2570 100 + 1
UAUCUGAAAGAUGCCUUGACUAUUAUUUAUAAUUUGUAUCCGAGAGUCAGGUACAA--ACAGCCAGGCAGCACUGACGCUAUCCGGAUGGCUGCGCUGGCUC
...........(((((.((((......(((.....)))......)))))))))...--..(((((((((((.(((........)))...))))).)))))). ( -30.70)
>DroEre_CAF1 2631 84 + 1
UAUCCGAGUGUAGGGUUAACCAU----------UUGCAC------AGCAGGUACAC--GCAGCCAGGCAGCACUGGCGGUAUCCGGAUGGCUGCGCUGGCUC
.....(.((((.((.....))((----------((((..------.))))))))))--.)(((((((((((.((((......))))...))))).)))))). ( -32.90)
>DroYak_CAF1 2799 79 + 1
UAUCUGAAUGUCGAU-------G----------UUCCAC------AUGAGGUACACAAGCAGCCAGCCAGCACUGACGCUAUCCGGAUGGCUGCGCUGGCUC
(((((..((((.(..-------.----------..).))------)).))))).......(((((((((((.(((........)))...)))).))))))). ( -26.00)
>consensus
UAUCUGAAAGAUGCCUUAACUAUUAUUUAUAAUUUGUAUCCGAGAGUCAGGUACAA__GCAGCCAGGCAGCACUGACGCUAUCCGGAUGGCUGCGCUGGCUC
..................................((((((.(.....).)))))).....(((((((((((.(((........)))...))))).)))))). (-19.52 = -21.08 +   1.56)

alignment

secondary structure

dotplot

Window 6

Location	4,333,676 – 4,333,776
Length	100
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	74.70
Mean single sequence MFE	-28.14
Consensus MFE	-17.88
Energy contribution	-19.28
Covariance contribution	1.40
Combinations/Pair	1.10
Mean z-score	-1.45
Structure conservation index	0.64
SVM decision value	0.07
SVM RNA-class probability	0.566813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4333676 100 - 22407834
GAGCCAGCGCAGCCAUCCGGAUAGCAAUAGUGCUGCCUGGCUGC--UUGUACCUGACUCUCGGAUACAAAUUAUAAAUAAUAGUUAACGCAUCUUUCAGAUA
......(((((((((...((.(((((....))))))))))))))--(((((.(((.....))).)))))...................))(((.....))). ( -28.10)
>DroSec_CAF1 2647 100 - 1
GAGCCAGCGCAGCCAUCCGGAUAGUGUCAGUGCUGCCUGGCUGC--UUGUACCUGACUCUCGGAUACAAAUUAUAAAUAAUAGUUAAGGCAUCUUUCAGAUA
..(((...(((((((...((.((((......)))))))))))))--(((((.(((.....))).)))))..................)))(((.....))). ( -28.90)
>DroSim_CAF1 2570 100 - 1
GAGCCAGCGCAGCCAUCCGGAUAGCGUCAGUGCUGCCUGGCUGU--UUGUACCUGACUCUCGGAUACAAAUUAUAAAUAAUAGUCAAGGCAUCUUUCAGAUA
..(((...(((((((...((.(((((....))))))))))))))--(((((.(((.....))).)))))..................)))(((.....))). ( -28.30)
>DroEre_CAF1 2631 84 - 1
GAGCCAGCGCAGCCAUCCGGAUACCGCCAGUGCUGCCUGGCUGC--GUGUACCUGCU------GUGCAA----------AUGGUUAACCCUACACUCGGAUA
.((((((((((((((..(((.(((.....))))))..)))))))--))((((.....------))))..----------.)))))...((.......))... ( -28.90)
>DroYak_CAF1 2799 79 - 1
GAGCCAGCGCAGCCAUCCGGAUAGCGUCAGUGCUGGCUGGCUGCUUGUGUACCUCAU------GUGGAA----------C-------AUCGACAUUCAGAUA
..(((((.(((((((.((((...((....)).)))).)))))))))).))..((.((------((.(..----------.-------..).))))..))... ( -26.50)
>consensus
GAGCCAGCGCAGCCAUCCGGAUAGCGUCAGUGCUGCCUGGCUGC__UUGUACCUGACUCUCGGAUACAAAUUAUAAAUAAUAGUUAACGCAUCUUUCAGAUA
.((((((.((((((...((.....))...).))))))))))).....((((.(((.....))).)))).................................. (-17.88 = -19.28 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:37 2006