Locus 6778

Sequence ID	X_DroMel_CAF1
Location	16,855,269 – 16,855,372
Length	103
Max. P	0.762331

overview

Window 2

Location	16,855,269 – 16,855,372
Length	103
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	84.14
Mean single sequence MFE	-21.32
Consensus MFE	-13.47
Energy contribution	-14.66
Covariance contribution	1.19
Combinations/Pair	1.06
Mean z-score	-1.65
Structure conservation index	0.63
SVM decision value	-0.06
SVM RNA-class probability	0.505531
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16855269 103 + 22224390
AAGAGCGGUACUCAU---CAUGCCCCGCCCAUCGUCCUCCGGUGAUGCAUAUAAGUCGUAACUAUCCCCACUCCCACCUGAGGCACCUGGAUCACCUGCACCAUCA
..((((((..(....---...)..))))(((..((((((.((((.........(((....)))...........)))).)))).)).))).))............. ( -20.35)
>DroSec_CAF1 53950 103 + 1
AUGAGCGGGACUCAU---CAUGCCCCGCCCAUCGUCCUUCUGUGAUGCAUAUAAGUCGUAACUAUCCCCACUCCCACCUGCGGCACCUGCAUCACCUGCACCAUCA
(((.(((((.(....---...).))))).))).........((((((((.....((((((..................))))))...))))))))........... ( -26.07)
>DroEre_CAF1 39235 94 + 1
AUGAGCGGGACUCAU---CUUGCUCCGCCCAUCGUUCUCCGGUGAUGCAUACAAGCCCUAACUAUCCCCACUCCCACC---------UGCAUCACCUGCACCAUCA
..((((((((....)---)))))))...............(((((((((.............................---------))))))))).......... ( -22.45)
>DroYak_CAF1 38692 97 + 1
AUGAGCGGAACUCAUCAUCAUGACCCGCCCAUCGUUCUCCGAUGAUGCAUAUAAGCCGUAACUUUGCCCACUUCCACC---------UGCAUCACCUGCACCAUCA
(((.((((...((((....)))).)))).)))........((((.((((...(((......)))(((...........---------.))).....)))).)))). ( -16.40)
>consensus
AUGAGCGGGACUCAU___CAUGCCCCGCCCAUCGUCCUCCGGUGAUGCAUAUAAGCCGUAACUAUCCCCACUCCCACC_________UGCAUCACCUGCACCAUCA
..(.(((((.(..........).))))).)..........(((((((((......................................))))))))).......... (-13.47 = -14.66 +   1.19)

alignment

secondary structure

dotplot

Window 3

Location	16,855,269 – 16,855,372
Length	103
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	84.14
Mean single sequence MFE	-33.55
Consensus MFE	-26.42
Energy contribution	-27.23
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-1.74
Structure conservation index	0.79
SVM decision value	0.51
SVM RNA-class probability	0.762331
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16855269 103 - 22224390
UGAUGGUGCAGGUGAUCCAGGUGCCUCAGGUGGGAGUGGGGAUAGUUACGACUUAUAUGCAUCACCGGAGGACGAUGGGCGGGGCAUG---AUGAGUACCGCUCUU
(((.((..(.((....))..)..)))))...(((((((((........).((((((((((..(.(((........)))..)..)))).---)))))).)))))))) ( -31.00)
>DroSec_CAF1 53950 103 - 1
UGAUGGUGCAGGUGAUGCAGGUGCCGCAGGUGGGAGUGGGGAUAGUUACGACUUAUAUGCAUCACAGAAGGACGAUGGGCGGGGCAUG---AUGAGUCCCGCUCAU
.....((.(..((((((((....(((....)))((((.(.........).))))...))))))))....).)).(((((((((((...---....))))))))))) ( -38.40)
>DroEre_CAF1 39235 94 - 1
UGAUGGUGCAGGUGAUGCA---------GGUGGGAGUGGGGAUAGUUAGGGCUUGUAUGCAUCACCGGAGAACGAUGGGCGGAGCAAG---AUGAGUCCCGCUCAU
.....((.(.(((((((((---------.(..((..(((......)))...))..).))))))))).)...)).((((((((..(...---....)..)))))))) ( -31.80)
>DroYak_CAF1 38692 97 - 1
UGAUGGUGCAGGUGAUGCA---------GGUGGAAGUGGGCAAAGUUACGGCUUAUAUGCAUCAUCGGAGAACGAUGGGCGGGUCAUGAUGAUGAGUUCCGCUCAU
.(((((((((.((((.((.---------.((((...(....)...)))).)))))).)))))))))........(((((((((((((....))))..))))))))) ( -33.00)
>consensus
UGAUGGUGCAGGUGAUGCA_________GGUGGGAGUGGGGAUAGUUACGACUUAUAUGCAUCACCGGAGAACGAUGGGCGGGGCAUG___AUGAGUCCCGCUCAU
..((.((.(.(((((((((..............((((.(.........).))))...)))))))))...).)).))(((((((((..........))))))))).. (-26.42 = -27.23 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:45 2006