Locus 276

Sequence ID	3R_DroMel_CAF1
Location	1,074,121 – 1,074,250
Length	129
Max. P	0.741237

overview

Window 6

Location	1,074,121 – 1,074,213
Length	92
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	82.03
Mean single sequence MFE	-32.88
Consensus MFE	-19.02
Energy contribution	-19.00
Covariance contribution	-0.02
Combinations/Pair	1.32
Mean z-score	-2.47
Structure conservation index	0.58
SVM decision value	0.37
SVM RNA-class probability	0.708299
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1074121 92 - 27905053
AUACCCC--ACUGCCCCCCACACACAGGGUGCAAAUUAGCACCCAGGGGAGCUGUGAAGGCAAAGUUUAUAAUGAGCUUGGCCA---GGAGGGGCCA
.......--...(((((((...(((.((((((......)))))).((....)))))..(((.((((((.....)))))).))).---)).))))).. ( -39.20)
>DroSec_CAF1 10196 87 - 1
AUACCCC--ACUCCC-----CACACAGGGCGCAAAUUAGCACCCAGGGGAGCUGUGAAGGCAAAGUUUAUAAUGAGCUUGGCCA---GGAGGGGCCA
...((((--.(((((-----(.....(((.((......)).))).)))))).......(((.((((((.....)))))).))).---...))))... ( -35.70)
>DroSim_CAF1 10312 87 - 1
AUACCCC--ACUCCC-----CACACAGGGCGCAAAUUAGCACCCAGGGGAGCUGUGAAGGCAAAGUUUAUAAUGAGCUUGGCCA---GGAGGGGCCA
...((((--.(((((-----(.....(((.((......)).))).)))))).......(((.((((((.....)))))).))).---...))))... ( -35.70)
>DroEre_CAF1 10530 85 - 1
-----CC--ACUCCC--GGACACAGAGAACGCAAAUUAGCACCCAGGGGAGCUGUGAAGGCAAAGUUUAUAAUGGGCUUGGCCA---GGGGGGUCCA
-----..--((((((--...(((((.....((......)).((....))..)))))..(((.((((((.....)))))).))).---.))))))... ( -28.80)
>DroYak_CAF1 16389 85 - 1
-----CG--CCGCCC--CUAUACAGAGGGCGCAAAUUACUACCCAGUGGAACUGUGAAGGCAAAGUUUAUAAUGAGCUUGGCCA---GGGGGGUCCA
-----.(--((.(((--((..........((((..(((((....)))))...))))..(((.((((((.....)))))).))))---)))))))... ( -27.00)
>DroAna_CAF1 11257 91 - 1
----CCCGGAUUCUU--CGGCACAGAGGGCGCAAAUUAGCACCCAGGGGAGCUUCGUGGGCAAAGUUUAUAAUGAGCUUGGUCAUAAGGGGGGUCCA
----...((((((((--(..(((...(((.((......)).)))(((....))).)))(((.((((((.....)))))).)))....))))))))). ( -30.90)
>consensus
____CCC__ACUCCC__C_ACACACAGGGCGCAAAUUAGCACCCAGGGGAGCUGUGAAGGCAAAGUUUAUAAUGAGCUUGGCCA___GGAGGGGCCA
..........((((........(((((...((......)).((....))..)))))..(((.((((((.....)))))).)))....))))...... (-19.02 = -19.00 +  -0.02)

alignment

secondary structure

dotplot

Window 7

Location	1,074,148 – 1,074,250
Length	102
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	74.05
Mean single sequence MFE	-31.82
Consensus MFE	-13.14
Energy contribution	-13.98
Covariance contribution	0.84
Combinations/Pair	1.30
Mean z-score	-1.86
Structure conservation index	0.41
SVM decision value	0.45
SVM RNA-class probability	0.741237
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1074148 102 + 27905053
AACUUUGCCUUCACAGCUCCCCUGGGUGCUAAUUUGCACCCUGUGUGUGGGGGGCAGUGGGGUAUUGGUAUUGGUAUUGGUAUAGGAAAAGGGACUUGGAUU---
..((((.(((((((.(((((((.((((((......)))))).......))))))).)))).((((..(((....)))..))))))).))))...........--- ( -39.60)
>DroSec_CAF1 10223 91 + 1
AACUUUGCCUUCACAGCUCCCCUGGGUGCUAAUUUGCGCCCUGUGUG-----GGGAGUGGGGUAUUGGU------AUUGGUAUAGGGACAGGGAUUGGGACU---
..(((((((((..(.(((((((.((((((......)))))).....)-----)))))).).(((((...------...))))))))).))))).........--- ( -33.70)
>DroSim_CAF1 10339 91 + 1
AACUUUGCCUUCACAGCUCCCCUGGGUGCUAAUUUGCGCCCUGUGUG-----GGGAGUGGGGUAUUGGU------AUUGGUAUAGGGACAGGGAUUGGGACU---
..(((((((((..(.(((((((.((((((......)))))).....)-----)))))).).(((((...------...))))))))).))))).........--- ( -33.70)
>DroEre_CAF1 10557 78 + 1
AACUUUGCCUUCACAGCUCCCCUGGGUGCUAAUUUGCGUUCUCUGUGUCC--GGGAGUGG------------------GGUAUUGGGAUUGGGAUUGG-------
..(..(.((.((.(((..((((.(..(((......)))..)((((....)--)))...))------------------))..))).))..)).)..).------- ( -20.80)
>DroYak_CAF1 16416 87 + 1
AACUUUGCCUUCACAGUUCCACUGGGUAGUAAUUUGCGCCCUCUGUAUAG--GGGCGGCG----------------UUGCUAUAAUGAGAGGGAUUGGGGCUCGU
......((((...(((((((.((..((((((((...((((((.......)--)))))..)----------------)))))))....)).))))))))))).... ( -31.30)
>consensus
AACUUUGCCUUCACAGCUCCCCUGGGUGCUAAUUUGCGCCCUGUGUGU____GGGAGUGGGGUAUUGGU______AUUGGUAUAGGGACAGGGAUUGGGACU___
..((...((((....((((((..((((((......))))))...........)))))).....................((......))))))...))....... (-13.14 = -13.98 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:18 2006