Locus 4048

Sequence ID	2L_DroMel_CAF1
Location	11,728,136 – 11,728,272
Length	136
Max. P	0.902876

overview

Window 5

Location	11,728,136 – 11,728,243
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	88.07
Mean single sequence MFE	-24.46
Consensus MFE	-17.08
Energy contribution	-18.12
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-2.14
Structure conservation index	0.70
SVM decision value	0.40
SVM RNA-class probability	0.719470
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11728136 107 - 22407834
CCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUACAGCCACACACCCACUUCCACACCCAUAUUAGAGAUGCG
....((((.((..((((.....))))..))(((..(((..(((((.....)))))..)))..)))....................................).))). ( -22.70)
>DroSec_CAF1 187557 105 - 1
CCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGGCACACACCCACAACCACACCCAUAUUAG--AUGCG
....((((.((..((((.....))))..))..((((((((((((((.........)))))....)))))))))..........................)--.))). ( -27.60)
>DroSim_CAF1 179804 105 - 1
CCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGGCACACACCCACAUCCACACCCAUAUUAG--AUGCG
....((((.((..((((.....))))..))..((((((((((((((.........)))))....)))))))))..........................)--.))). ( -27.60)
>DroEre_CAF1 205445 96 - 1
CCAAGCACAGAUGCUUUUCAAAGAAGUGGGAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGCCAC--ACCCACAUC-------GUAAUAG--AUGCG
..(((((....)))))......((.(((((.(((.(((((((((((.........)))))....)))))))))..--.))))).))-------(((....--.))). ( -24.50)
>DroYak_CAF1 179838 97 - 1
CC------AGCUGCUUUUCAAAGGAGUGCCAGGCCUGAAAAUGACUCCCAGUCAUAGUCACUCCUUUUCAGUCAC--ACCCACAUCCACACCCUUAGUAG--AUGCG
..------.((((......((((((((((((....))...(((((.....))))).).))))))))).))))...--.....((((.((.......)).)--))).. ( -19.90)
>consensus
CCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGCCACACACCCACAUCCACACCCAUAUUAG__AUGCG
....(((..((((((((.....))))))))(((..(((..(((((.....)))))..)))..)))......................................))). (-17.08 = -18.12 +   1.04)

alignment

secondary structure

dotplot

Window 6

Location	11,728,165 – 11,728,272
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	92.13
Mean single sequence MFE	-34.84
Consensus MFE	-27.64
Energy contribution	-28.16
Covariance contribution	0.52
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.79
SVM decision value	1.03
SVM RNA-class probability	0.902876
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11728165 107 + 22407834
UGUGUGGCUGUAAAGGAGUGACUAUGACUAGGAGUCAUUUUCAGGCCUGCCACUUCUUUGAAAAGCAGCUGUGCUUGGCUGAAAGCCGCAGUUGAUUUGCAAAGCCC
...(((((.....(((..(((..(((((.....)))))..)))..))))))))..(((((.....(((((((((((......))).)))))))).....)))))... ( -38.00)
>DroSec_CAF1 187584 107 + 1
UGUGUGCCUGAAAAGGAGUGACUAUGACUAGGAGUCAUUUUCAGGCCUGCCACUUCUUUGAAAAGCAGCUGUGCUUGGCUCAAAGCCGCAGUUGAUUUGCAAAGCCC
.(((.((((((....((((((((.........))))))))))))))....)))..(((((.....(((((((((((......))).)))))))).....)))))... ( -35.30)
>DroSim_CAF1 179831 107 + 1
UGUGUGCCUGAAAAGGAGUGACUAUGACUAGGAGUCAUUUUCAGGCCUGCCACUUCUUUGAAAAGCAGCUGUGCUUGGCUCAAAGCCGCAGUUGAUUUGCAAAGCCC
.(((.((((((....((((((((.........))))))))))))))....)))..(((((.....(((((((((((......))).)))))))).....)))))... ( -35.30)
>DroEre_CAF1 205465 105 + 1
U--GUGGCUGAAAAGGAGUGACUAUGACUAGGAGUCAUUUUCAGGCCUCCCACUUCUUUGAAAAGCAUCUGUGCUUGGCUCAAAGCCGCAGUUGAUUUGCAAAGCCC
.--..((((..((((((((((..(((((.....)))))..)).((....))))))))))...(((((....)))))(((.....)))((((.....))))..)))). ( -30.90)
>DroYak_CAF1 179865 99 + 1
U--GUGACUGAAAAGGAGUGACUAUGACUGGGAGUCAUUUUCAGGCCUGGCACUCCUUUGAAAAGCAGCU------GGUUCAAAGCCGCUGCUGAUUUGCAAAGCCC
(--(..(....(((((((((.(((.(.(((..((...))..))).).))))))))))))....((((((.------(((.....)))))))))...)..))...... ( -34.70)
>consensus
UGUGUGCCUGAAAAGGAGUGACUAUGACUAGGAGUCAUUUUCAGGCCUGCCACUUCUUUGAAAAGCAGCUGUGCUUGGCUCAAAGCCGCAGUUGAUUUGCAAAGCCC
...(((.......(((..(((..(((((.....)))))..)))..)))..)))..(((((.....(((((((....(((.....)))))))))).....)))))... (-27.64 = -28.16 +   0.52)

alignment

secondary structure

dotplot

Window 7

Location	11,728,165 – 11,728,272
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	92.13
Mean single sequence MFE	-32.30
Consensus MFE	-23.14
Energy contribution	-23.98
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.22
Structure conservation index	0.72
SVM decision value	0.17
SVM RNA-class probability	0.618454
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11728165 107 - 22407834
GGGCUUUGCAAAUCAACUGCGGCUUUCAGCCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUACAGCCACACA
.((((..(((.......)))(((.....))).......((..((((.....))))..))(((..(((..(((((.....)))))..)))..)))....))))..... ( -31.20)
>DroSec_CAF1 187584 107 - 1
GGGCUUUGCAAAUCAACUGCGGCUUUGAGCCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGGCACACA
..((((.(((.......)))(((.....)))))))...((..((((.....))))..))..((((((((((((((.........)))))....)))))))))..... ( -34.50)
>DroSim_CAF1 179831 107 - 1
GGGCUUUGCAAAUCAACUGCGGCUUUGAGCCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGGCACACA
..((((.(((.......)))(((.....)))))))...((..((((.....))))..))..((((((((((((((.........)))))....)))))))))..... ( -34.50)
>DroEre_CAF1 205465 105 - 1
GGGCUUUGCAAAUCAACUGCGGCUUUGAGCCAAGCACAGAUGCUUUUCAAAGAAGUGGGAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGCCAC--A
.((((...........(..(..(((((((..(((((....))))))))))))..)..)((((..(((..(((((.....)))))..)))..))))...))))..--. ( -32.70)
>DroYak_CAF1 179865 99 - 1
GGGCUUUGCAAAUCAGCAGCGGCUUUGAACC------AGCUGCUUUUCAAAGGAGUGCCAGGCCUGAAAAUGACUCCCAGUCAUAGUCACUCCUUUUCAGUCAC--A
...(((((.(((..((((((((.......))------.))))))))))))))((.((..(((..(((..(((((.....)))))..)))..)))...)).))..--. ( -28.60)
>consensus
GGGCUUUGCAAAUCAACUGCGGCUUUGAGCCAAGCACAGCUGCUUUUCAAAGAAGUGGCAGGCCUGAAAAUGACUCCUAGUCAUAGUCACUCCUUUUCAGCCACACA
((((((.(((.......)))(((.....))).......((((((((.....))))))))))))))((..(((((.....)))))..))................... (-23.14 = -23.98 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:59 2006