Locus 5489

Sequence ID	2R_DroMel_CAF1
Location	17,649,667 – 17,649,860
Length	193
Max. P	0.908918

overview

Window 6

Location	17,649,667 – 17,649,781
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.40
Mean single sequence MFE	-37.26
Consensus MFE	-29.94
Energy contribution	-30.02
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.39
Structure conservation index	0.80
SVM decision value	0.04
SVM RNA-class probability	0.553870
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17649667 114 + 20766785
UCAAAUUAGCUGCAGCAGCAGCAGUGGGCACUACAACAAAACACUUGCUUGUCUGCCACCGCGUUGCA------GUUGCAUCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCG
........(((((....))))).(((((((..(((((((.....))).)))).)))).((((((((((------.(((.......))).).)))))))))))).....(((.....))). ( -40.20)
>DroSec_CAF1 3284 114 + 1
UCAAAUUAGCUGCAGCACCAGGAGCAGCCACUACAACAAAACACUUGCUUGUCUGCCACCGCGUUGCA------GUUGCAUCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCG
........(((((..........)))))..................(((.(((((((((.(.((((((------.((((..((....))..)))))))))).).))))..))))).))). ( -34.80)
>DroSim_CAF1 9202 114 + 1
UCAAAUUAGCUGCAGCACCAGCAGCAGCCACUACAACAAAACACUUGCUUGUCUGCCACCGCGUUGCA------GUUGCAUCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCG
........(((((.((....)).)))))..................(((.(((((((((.(.((((((------.((((..((....))..)))))))))).).))))..))))).))). ( -38.00)
>DroEre_CAF1 3375 108 + 1
UCAAAUUAGCUGCAGCA------GCAGCCACUACAACAAAACACUUGCUUGUCUGCCACCGCGUUGCA------GUUGCAUCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCG
........(((((....------)))))..................(((.(((((((((.(.((((((------.((((..((....))..)))))))))).).))))..))))).))). ( -35.70)
>DroYak_CAF1 14615 114 + 1
UCAAAUUAGCUGCAGCA------GCAGCGACUACAACAAAACACUUGCUUGUCUGACACCGCGUUGCAGUUGCAGUUGCAUCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCA
........(((((....------))))).................((((.(((((.(.((((..(((....)))(((((((...((....))..)))))))...))))).))))).)))) ( -37.60)
>consensus
UCAAAUUAGCUGCAGCA_CAG_AGCAGCCACUACAACAAAACACUUGCUUGUCUGCCACCGCGUUGCA______GUUGCAUCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCG
........(((((..........)))))..................(((.(((((((((.(.((((((......((..(.........)..))..)))))).).))))..))))).))). (-29.94 = -30.02 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	17,649,741 – 17,649,860
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.57
Mean single sequence MFE	-36.81
Consensus MFE	-32.62
Energy contribution	-32.46
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.57
Structure conservation index	0.89
SVM decision value	1.06
SVM RNA-class probability	0.908918
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17649741 119 + 20766785
UCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCGCUGUAAUUAACUAUUAACACGAGUG-CUCCGAUUGUGCCACAAAUGAGCAAUUGCCGAGAGCUUAUCAAAUGGAGUAGAA
(((((((..(((((((((((((((((.((.......((((((.((((.....)))).....))))-)))).)))))))).(....).)).))))))).((.....))...))))..))). ( -36.11)
>DroSec_CAF1 3358 119 + 1
UCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCGCCGUAAUUAACUAUUAACAUGAGUG-CUCCGAUUGUGCCACAAAUGAGCAAUUGCCGAGAGCUUAUCAAAUGGAGUAGAA
(((((((..(((((((((((((((((.((.......((((((((..............))).)))-)))).)))))))).(....).)).))))))).((.....))...))))..))). ( -35.55)
>DroSim_CAF1 9276 119 + 1
UCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCGCUGUAAUUAACUAUUAACAUGAGUG-CUCCGAUUGUGCCACAAAUGAGCAAUUGCCGAGAGCUUAUCAAAUGGAGUAGAA
(((((((..(((((((((((((((((.((.......((((((.((((.....)))).....))))-)))).)))))))).(....).)).))))))).((.....))...))))..))). ( -36.11)
>DroEre_CAF1 3443 119 + 1
UCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCGCGGCAAUUAACUAUUACCAUGAGUG-CUGCGAUUGUGCCACAAAUGAGCAAUUGCCGAGAGCUUAUCAAAUGGAGUGGAA
(((((((.((((((.((((((((.(((((((.....)))..(........).....))))..)))-)))))....))))))..((((((...........))))))....))))..))). ( -40.70)
>DroYak_CAF1 14689 120 + 1
UCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCAGUGUAAUUAACUAUUAACAUGAGUGGCUGCGAUUGUGCCACAAAUGAGCAAUUGCCGAGAGCUUAUCAAAUGGAGUAGAA
(((((((..((..((.(((((.......)))...((((((((.((((.....)))).(((..(((((.........)))))..)))....))))))))..))))..))..))))..))). ( -35.60)
>consensus
UCUUCCAAGUGGCAAUGCGGCACAGUGGGCCAGAUCGGCGCUGUAAUUAACUAUUAACAUGAGUG_CUCCGAUUGUGCCACAAAUGAGCAAUUGCCGAGAGCUUAUCAAAUGGAGUAGAA
(((((((..(((((((((((((((((.((((.....)))..........(((.........))).....).)))))))).(....).)).))))))).((.....))...))))..))). (-32.62 = -32.46 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:09 2006