Locus 5217

Sequence ID	X_DroMel_CAF1
Location	13,622,649 – 13,622,851
Length	202
Max. P	0.877285

overview

Window 8

Location	13,622,649 – 13,622,740
Length	91
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	93.48
Mean single sequence MFE	-16.92
Consensus MFE	-14.20
Energy contribution	-14.20
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.84
SVM decision value	0.90
SVM RNA-class probability	0.877285
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13622649 91 - 22224390
CCACACCCUCGCGAAUGCCAGAGCAUCCUUCUAGAUGGGC--AAAAAUCCUUCAAAGUUCAGAAACAGAACAACAGGCAACAAAAUCAUCGCC
..........((((.((((....((((......)))))))--).............((((.......))))....(....).......)))). ( -16.10)
>DroSec_CAF1 8347 92 - 1
CCACACGCUCGCGAAUGCCAGAGCAUCCUUCUAGAUGGUC-GAAAAAUCCUUCAAAGUUCAGAAACAGAACAACAGGCAACAAAAUCAUCGCC
..........((((.((((.((.((((......)))).))-...............((((.......))))....)))).........)))). ( -18.00)
>DroSim_CAF1 8412 93 - 1
CCACACGCUCGCGAAUGCCAGAGCAUCCUUCUAGAUGGGCAGAAAAAUCCUUCAAAGUUCAGAAACAGAACAACAGGCAACAAAAUCAUCGCC
..........((((.((((....((((......))))))))((.............((((.......))))....(....)....)).)))). ( -16.80)
>DroEre_CAF1 8344 90 - 1
CUAUACACUCGCGAAUGCCAGAGCAUCCUCCUAGAUGGG---GAAAAUCCUUCAAAGUUCAAAAACAGAACAACAGGCAACCAAAUCAUCGCC
..........((((.((((.((...(((.((.....)))---))...)).......((((.......))))....)))).........)))). ( -17.50)
>DroYak_CAF1 7799 90 - 1
CAACACACUCGCGAAUGCCAGAGCAUCCUCCUAGAUGGG---AAAAAUCCUUCAAAGUUCACAAACAGAACAACAGGCAACAAAAUCAUCGCC
..........((((.((((.(((((((......))))((---(....))))))...((((.......))))....)))).........)))). ( -16.20)
>consensus
CCACACACUCGCGAAUGCCAGAGCAUCCUUCUAGAUGGGC__AAAAAUCCUUCAAAGUUCAGAAACAGAACAACAGGCAACAAAAUCAUCGCC
..........((((.((((....((((......))))...................((((.......))))....)))).........)))). (-14.20 = -14.20 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	13,622,740 – 13,622,851
Length	111
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	94.60
Mean single sequence MFE	-27.16
Consensus MFE	-22.94
Energy contribution	-24.02
Covariance contribution	1.08
Combinations/Pair	1.04
Mean z-score	-1.36
Structure conservation index	0.84
SVM decision value	0.23
SVM RNA-class probability	0.643871
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13622740 111 + 22224390
-----AAAACUCGCCAUACACAAACACAUGCCCACAGGGCCACGCAUAAUACACAUGCAAAUGUCAAAGCUGCCAGGCUGUCGCCAUAAGCGAAAGCGUCACUUGUGCCACCUUAC
-----.............(((((......((((...)))).((((.......((((....))))....(((....(((....)))...)))....))))...)))))......... ( -23.00)
>DroSec_CAF1 8451 114 + 1
CGGCGAAAACUCGUCAUA--CAAACACAUGUCCACAGGGCCACGCAUAAUACACAUGCAAAUGUCAAAGCUGCCAGGCUGUCGCCAUAAGCGAAAGCGUCACUUGUGCCACCUUAC
.(((((....)))))...--............((((((...((((.......((((....))))....(((....(((....)))...)))....))))..))))))......... ( -27.60)
>DroSim_CAF1 8515 114 + 1
CGGCGAAAACUCGCCAUA--CAAACACAUGUCCACAGGGCCACGCAUAAUACACAUGCAAAUGUCAAAGCUGCCAGGCUGUCGCCAUAAGCGAAAGCGUCACUUGUGCCACCUUAC
.(((((....)))))...--............((((((...((((.......((((....))))....(((....(((....)))...)))....))))..))))))......... ( -30.30)
>DroEre_CAF1 8448 114 + 1
UGGCGUAAACUCGCCAUA--CAAACACAUGCCCAGAGGACCACGCAUAAUACACAUGCAAAUGUCAAAGCUGCCAGGCUGUCGCCAUAAGCGAAAGCGUCACUUGUGCCACCUUAC
(((((......)))))..--..............((((..(((((((.......))))........(((.((.(.(((....)))....((....))).))))))))...)))).. ( -27.00)
>DroYak_CAF1 7923 114 + 1
UGGCGACAACUCGCCAUA--CAAACACAUGCCCAGAGGACCACGCAUAAUACACAUGCAAAUGUCAAAGCUGCCAGGCUGUCGCCAUAAGCGAAAGCGUCACUUGUGCCACCUUAC
((((((....))))))..--..............((((..(((((((.......))))........(((.((.(.(((....)))....((....))).))))))))...)))).. ( -27.90)
>consensus
CGGCGAAAACUCGCCAUA__CAAACACAUGCCCACAGGGCCACGCAUAAUACACAUGCAAAUGUCAAAGCUGCCAGGCUGUCGCCAUAAGCGAAAGCGUCACUUGUGCCACCUUAC
.((((......)))).................((((((...((((.......((((....))))....(((....(((....)))...)))....))))..))))))......... (-22.94 = -24.02 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:34 2006