Locus 4726

Sequence ID	3R_DroMel_CAF1
Location	12,409,607 – 12,409,736
Length	129
Max. P	0.999998

overview

Window 2

Location	12,409,607 – 12,409,701
Length	94
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	70.19
Mean single sequence MFE	-30.15
Consensus MFE	-21.65
Energy contribution	-21.67
Covariance contribution	0.01
Combinations/Pair	1.29
Mean z-score	-2.83
Structure conservation index	0.72
SVM decision value	6.34
SVM RNA-class probability	0.999998
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12409607 94 - 27905053
G-------------------CGAUGCCGAUG-UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCACUACAUCUACUCAUACACUUACUCACACACGCAC
(-------------------(((.((((...-..))))))))...((((((.((((((((......)).)))))).))))))................................ ( -30.40)
>DroSim_CAF1 8237 94 - 1
G-------------------CGAUGCCGAUG-UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCACUACAUCUACUCAUACACUUACUCACACACGCAC
(-------------------(((.((((...-..))))))))...((((((.((((((((......)).)))))).))))))................................ ( -30.40)
>DroAna_CAF1 8959 108 - 1
-CUAUAGCAGUAGCUGUAGCUGGAGCUGAAGCCUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAAUAAACUGCACACACACCAUGGA-----ACACCUCGCCACACACACAC
-(((((((....)))))))...(((((((....)))))))......(((..(((((((......................)))))))..-----.)))................ ( -29.65)
>consensus
G___________________CGAUGCCGAUG_UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCACUACAUCUACUCAUACACUUACUCACACACGCAC
....................(((.(((((....)))))))).....(((((.((((((((......)).)))))).)))))................................. (-21.65 = -21.67 +   0.01)

alignment

secondary structure

dotplot

Window 3

Location	12,409,641 – 12,409,736
Length	95
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	81.43
Mean single sequence MFE	-34.90
Consensus MFE	-23.16
Energy contribution	-22.73
Covariance contribution	-0.44
Combinations/Pair	1.19
Mean z-score	-1.82
Structure conservation index	0.66
SVM decision value	0.40
SVM RNA-class probability	0.721475
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12409641 95 - 27905053
CCCACGAGCAAAUAUGCCGCAUGCUGAUGACGACGG-------------------CGAUGCCGAUG-UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCA
...((((((.(((((.(.((((((((.......)))-------------------).)))).))))-))..)))))).....((((.((((((((......)).)))))).)))) ( -34.10)
>DroSec_CAF1 8630 95 - 1
CCCACGAGCAAAUAUGCCGCAUGCUGAUGACGACGG-------------------CGAUGCCGAUG-UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCA
...((((((.(((((.(.((((((((.......)))-------------------).)))).))))-))..)))))).....((((.((((((((......)).)))))).)))) ( -34.10)
>DroSim_CAF1 8271 95 - 1
CCCACGAGCAAAUAUGCCGCAUGCUGAUGACGACGG-------------------CGAUGCCGAUG-UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCA
...((((((.(((((.(.((((((((.......)))-------------------).)))).))))-))..)))))).....((((.((((((((......)).)))))).)))) ( -34.10)
>DroAna_CAF1 8988 114 - 1
CCCAUGACCAAAUAUGCCGCAUGCUGAUGCUGAUG-CUAUAGCAGUAGCUGUAGCUGGAGCUGAAGCCUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAAUAAACUGCACACA
...............((((((((.((.(((((..(-(((((((....))))))))..(((((((....)))))))....)))))))))).))))).................... ( -37.30)
>consensus
CCCACGAGCAAAUAUGCCGCAUGCUGAUGACGACGG___________________CGAUGCCGAUG_UUCGGCUCGUAACAGUGCACGUGGUGGCCAAAAAGCACGCUACAUGCA
..((((.(((....((((((((....))).))........................((.(((((....))))))))))....))).))))(((((..........)))))..... (-23.16 = -22.73 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:29 2006