Locus 5922

Sequence ID	2L_DroMel_CAF1
Location	16,707,511 – 16,707,649
Length	138
Max. P	0.990811

overview

Window 4

Location	16,707,511 – 16,707,609
Length	98
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	79.29
Mean single sequence MFE	-37.73
Consensus MFE	-25.73
Energy contribution	-24.63
Covariance contribution	-1.10
Combinations/Pair	1.20
Mean z-score	-2.62
Structure conservation index	0.68
SVM decision value	2.23
SVM RNA-class probability	0.990811
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16707511 98 + 22407834
GAGUGCAGGGAACCAAGGGGUGCCAAUGUGCAAU-AUCCCGAUGGCCAUAAU------------------GGCCACUAUGGCCACCGUCCAUUUCCUGUUCUUUUGGCACGA---CUAUU
..((((.((((((...(((((((......)))..-.))))(((((......(------------------((((.....))))))))))........))))))...))))..---..... ( -31.30)
>DroSec_CAF1 162100 99 + 1
GAGUGCAGGGAGCCAAGGGGUGCCAAUGUGCGAUAAUCCCGAUGGCCAUAAU------------------GGCCACUAUGGCCGCCGUCCAUUUCCUGUUCUUUUGGCACGA---CUAUU
..((((.((((((...(((((((......))....)))))((((((......------------------((((.....))))))))))........))))))...))))..---..... ( -32.50)
>DroEre_CAF1 163252 119 + 1
GAGUGCAAAGAACCAAGGGGUGGCCAUGUGCAAU-AUCACAAUGGCCAUAAUGGCCACAAUGGUCAUAAUGGCCACAAUGGCCACCGACUAUUUCCUGUUCUUUUGGCAUGAUUACUAUU
..((((.((((((..(((((((((((((((....-..)))..(((((((.((((((.....)))))).)))))))..)))))))))........)))))))))...)))).......... ( -49.40)
>consensus
GAGUGCAGGGAACCAAGGGGUGCCAAUGUGCAAU_AUCCCGAUGGCCAUAAU__________________GGCCACUAUGGCCACCGUCCAUUUCCUGUUCUUUUGGCACGA___CUAUU
..((((.((((((...(..(((...(((.((.((.......)).))))).....................((((.....))))......)))..)..))))))...)))).......... (-25.73 = -24.63 +  -1.10)

alignment

secondary structure

dotplot

Window 5

Location	16,707,511 – 16,707,609
Length	98
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.29
Mean single sequence MFE	-35.91
Consensus MFE	-21.94
Energy contribution	-23.38
Covariance contribution	1.45
Combinations/Pair	1.04
Mean z-score	-2.28
Structure conservation index	0.61
SVM decision value	0.99
SVM RNA-class probability	0.895774
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16707511 98 - 22407834
AAUAG---UCGUGCCAAAAGAACAGGAAAUGGACGGUGGCCAUAGUGGCC------------------AUUAUGGCCAUCGGGAU-AUUGCACAUUGGCACCCCUUGGUUCCCUGCACUC
.....---..((((.....(((((((.((((..(((((((((((((....------------------)))))))))))))...)-)))((......))...)))..))))...)))).. ( -33.60)
>DroSec_CAF1 162100 99 - 1
AAUAG---UCGUGCCAAAAGAACAGGAAAUGGACGGCGGCCAUAGUGGCC------------------AUUAUGGCCAUCGGGAUUAUCGCACAUUGGCACCCCUUGGCUCCCUGCACUC
....(---((((.(((.............))))))))(((((((((....------------------)))))))))...((((.....((.((..((...))..))))))))....... ( -29.72)
>DroEre_CAF1 163252 119 - 1
AAUAGUAAUCAUGCCAAAAGAACAGGAAAUAGUCGGUGGCCAUUGUGGCCAUUAUGACCAUUGUGGCCAUUAUGGCCAUUGUGAU-AUUGCACAUGGCCACCCCUUGGUUCUUUGCACUC
...........(((..((((((((((........((((((((..((((((((.(((.((.....)).))).))))))))((((..-....)))))))))))))))..))))))))))... ( -44.40)
>consensus
AAUAG___UCGUGCCAAAAGAACAGGAAAUGGACGGUGGCCAUAGUGGCC__________________AUUAUGGCCAUCGGGAU_AUUGCACAUUGGCACCCCUUGGUUCCCUGCACUC
..........((((.....(((((((.......(((((((((((((......................)))))))))))))........((......))...)))..))))...)))).. (-21.94 = -23.38 +   1.45)

alignment

secondary structure

dotplot

Window 6

Location	16,707,550 – 16,707,649
Length	99
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.48
Mean single sequence MFE	-33.24
Consensus MFE	-21.19
Energy contribution	-21.75
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.35
Structure conservation index	0.64
SVM decision value	0.44
SVM RNA-class probability	0.738974
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16707550 99 - 22407834
UAUAAUAUUUGCAUUUGUAUUGGCUACGUGGCGUAUGCGUAAUAG---UCGUGCCAAAAGAACAGGAAAUGGACGGUGGCCAUAGUGGCC------------------AUUAUGGCCAUC
.....(((((.(..((.(.(((((.(((..(((....))).....---.)))))))).).))..).)))))...((((((((((((....------------------)))))))))))) ( -31.10)
>DroSec_CAF1 162140 99 - 1
UAUAAUAUUUGCAUUUGUAUUGGCUACGUGGCGUAUGCGUAAUAG---UCGUGCCAAAAGAACAGGAAAUGGACGGCGGCCAUAGUGGCC------------------AUUAUGGCCAUC
.....(((((((((.(((..((....))..))).))))).))))(---((((.(((.............))))))))(((((((((....------------------)))))))))... ( -29.52)
>DroEre_CAF1 163291 120 - 1
UAUAAUAUUUGCAUUUGUAUUGGGUACGUGGCGUAUGCGUAAUAGUAAUCAUGCCAAAAGAACAGGAAAUAGUCGGUGGCCAUUGUGGCCAUUAUGACCAUUGUGGCCAUUAUGGCCAUU
.....(((((.(....((((...)))).((((((.(((......)))...))))))........).)))))...(((((((((.((((((((.((....)).)))))))).))))))))) ( -39.10)
>consensus
UAUAAUAUUUGCAUUUGUAUUGGCUACGUGGCGUAUGCGUAAUAG___UCGUGCCAAAAGAACAGGAAAUGGACGGUGGCCAUAGUGGCC__________________AUUAUGGCCAUC
.....(((((.(..((.(.(((((((((((.....))))))...........))))).).))..).)))))...((((((((((((......................)))))))))))) (-21.19 = -21.75 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:39 2006