Locus 3

Sequence ID	3R_DroMel_CAF1
Location	63,593 – 63,692
Length	99
Max. P	0.995898

overview

Window 4

Location	63,593 – 63,692
Length	99
Sequences	3
Columns	99
Reading direction	forward
Mean pairwise identity	76.06
Mean single sequence MFE	-24.07
Consensus MFE	-15.16
Energy contribution	-15.16
Covariance contribution	0.01
Combinations/Pair	1.16
Mean z-score	-1.67
Structure conservation index	0.63
SVM decision value	0.52
SVM RNA-class probability	0.766530
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 63593 99 + 27905053
AAAUAAGCGUAAGUAAGGAGCAGAUCGCGCUGACAUCGAUGGGAUAGGUGCGGUGCUUAUGCAGUGGCACCCAGAAGGCUGGGAGAGAAGGGUACGAAG
......((((((((.........((((((((...(((.....))).)))))))))))))))).(((.(.(((((....))))).......).))).... ( -28.70)
>DroSec_CAF1 4994 81 + 1
ACAUAAGCGUAAGUAAGCAAAUAAGUGUGCUGACAUCGCUGGAAU-------------AUGCAGUGGCGCCCAGAAGUC-----GUAAAGGGCACGAAG
......((((.((((.((......)).)))).))..(((((....-------------...)))))))((((.......-----.....))))...... ( -19.20)
>DroSim_CAF1 8831 86 + 1
ACAUAAGCGUAAGUAAGCAAAUAAGUGUGCUGACAUCGCUGGGAU-------------AUGCAGUGGCGCCCAGAAGGCUGGGAGUAAAGGGCACGAAG
......((........))......((((.((.....(((((....-------------...)))))((.(((((....))))).))..)).)))).... ( -24.30)
>consensus
ACAUAAGCGUAAGUAAGCAAAUAAGUGUGCUGACAUCGCUGGGAU_____________AUGCAGUGGCGCCCAGAAGGCUGGGAGUAAAGGGCACGAAG
......((((.((((.((......)).)))).))..(((((.(.(((((.....)))))).)))))))((((.................))))...... (-15.16 = -15.16 +   0.01)

alignment

secondary structure

dotplot

Window 5

Location	63,593 – 63,692
Length	99
Sequences	3
Columns	99
Reading direction	reverse
Mean pairwise identity	76.06
Mean single sequence MFE	-19.92
Consensus MFE	-14.63
Energy contribution	-14.63
Covariance contribution	0.00
Combinations/Pair	1.12
Mean z-score	-2.18
Structure conservation index	0.73
SVM decision value	2.63
SVM RNA-class probability	0.995898
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 63593 99 - 27905053
CUUCGUACCCUUCUCUCCCAGCCUUCUGGGUGCCACUGCAUAAGCACCGCACCUAUCCCAUCGAUGUCAGCGCGAUCUGCUCCUUACUUACGCUUAUUU
....((((((.................))))))......((((((...((...((((.....))))...))((.....))...........)))))).. ( -17.33)
>DroSec_CAF1 4994 81 - 1
CUUCGUGCCCUUUAC-----GACUUCUGGGCGCCACUGCAU-------------AUUCCAGCGAUGUCAGCACACUUAUUUGCUUACUUACGCUUAUGU
....((((((.....-----.......))))))....((((-------------(....((((..((.((((........)))).))...))))))))) ( -21.40)
>DroSim_CAF1 8831 86 - 1
CUUCGUGCCCUUUACUCCCAGCCUUCUGGGCGCCACUGCAU-------------AUCCCAGCGAUGUCAGCACACUUAUUUGCUUACUUACGCUUAUGU
....((((((.................))))))....((((-------------(....((((..((.((((........)))).))...))))))))) ( -21.03)
>consensus
CUUCGUGCCCUUUACUCCCAGCCUUCUGGGCGCCACUGCAU_____________AUCCCAGCGAUGUCAGCACACUUAUUUGCUUACUUACGCUUAUGU
....((((((.................))))))..........................((((..((.((((........)))).))...))))..... (-14.63 = -14.63 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:49 2006