Locus 4223

Sequence ID 2R_DroMel_CAF1
Location 13,888,035 – 13,888,135
Length 100
Max. P 0.975590
window6782 window6783

overview

Window 2

Location 13,888,035 – 13,888,135
Length 100
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 78.24
Mean single sequence MFE -34.90
Consensus MFE -28.30
Energy contribution -28.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.81
SVM decision value 1.75
SVM RNA-class probability 0.975590
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13888035 100 + 20766785
AUGGGAAGGAGCAGUAGAGCAG-------------------GGGCGUGGGGGGGUUGUGUGUGUGUGCGGGAAGGACACGCACGUCCUGGGCCCAAGGGUGCUCAGGCAAACAACAUUU
..........((....(((((.-------------------((((.(((((......(((((((((.(.....).)))))))))))))).)))).....)))))..))........... ( -35.70)
>DroSec_CAF1 173897 113 + 1
AUGGAAAGGAGCAG-GGAGCAGGAGGGAGGGGGGGGGGGGGGUGCGUGAGGG-----AGUGUGUGUACGGAAAGGACACGCACGUCCUGGGCCCAAGGGUGCUCAGGCAAACAACAUUU
..........((..-...))................(..(..(((.((((((-----(((((((((.(.....).)))))))).)))...(((....))).)))).)))..)..).... ( -34.70)
>DroSim_CAF1 177691 99 + 1
AUGGGAAG---CAG-UAAGCAG-----------GGGAGGGGGUGCGUGGGGG-----AGUGUGUGUGCGGAAAGGACACGCACGUCCUGGGCCCAAGGGUGCUCAGGCAAACAACAUUU
.......(---(..-...))..-----------......(..(((.((((((-----(((((((((.(.....).)))))))).)))...(((....))).)))).)))..)....... ( -34.30)
>consensus
AUGGGAAGGAGCAG_AGAGCAG___________GGG_GGGGGUGCGUGGGGG_____AGUGUGUGUGCGGAAAGGACACGCACGUCCUGGGCCCAAGGGUGCUCAGGCAAACAACAUUU
.............................................(((..(.......((((((((.(.....).))))))))(.(((((((((...)).))))))))...)..))).. (-28.30 = -28.30 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,888,035 – 13,888,135
Length 100
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 78.24
Mean single sequence MFE -22.61
Consensus MFE -18.47
Energy contribution -18.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.82
SVM decision value 0.92
SVM RNA-class probability 0.882414
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13888035 100 - 20766785
AAAUGUUGUUUGCCUGAGCACCCUUGGGCCCAGGACGUGCGUGUCCUUCCCGCACACACACACAACCCCCCCACGCCC-------------------CUGCUCUACUGCUCCUUCCCAU
....(((((.((((((.((.((...)))).))))..(((((.(.....).)))))...)).)))))............-------------------..((......)).......... ( -22.60)
>DroSec_CAF1 173897 113 - 1
AAAUGUUGUUUGCCUGAGCACCCUUGGGCCCAGGACGUGCGUGUCCUUUCCGUACACACACU-----CCCUCACGCACCCCCCCCCCCCCCUCCCUCCUGCUCC-CUGCUCCUUUCCAU
...............(((((.....(((..(((((.(((((((........((....))...-----....))))))).................)))))..))-))))))........ ( -23.53)
>DroSim_CAF1 177691 99 - 1
AAAUGUUGUUUGCCUGAGCACCCUUGGGCCCAGGACGUGCGUGUCCUUUCCGCACACACACU-----CCCCCACGCACCCCCUCCC-----------CUGCUUA-CUG---CUUCCCAU
...........((.((((((.....(((...(((..(((((((...................-----....)))))))..))).))-----------)))))))-..)---)....... ( -21.70)
>consensus
AAAUGUUGUUUGCCUGAGCACCCUUGGGCCCAGGACGUGCGUGUCCUUUCCGCACACACACU_____CCCCCACGCACCCCC_CCC___________CUGCUCA_CUGCUCCUUCCCAU
....(((.(..(((..((....))..)))..).)))(((.((((.(.....).)))).))).......................................................... (-18.47 = -18.47 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:38 2006