Locus 5236

Sequence ID	3R_DroMel_CAF1
Location	13,687,518 – 13,687,637
Length	119
Max. P	0.772603

overview

Window 2

Location	13,687,518 – 13,687,637
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	83.84
Mean single sequence MFE	-36.85
Consensus MFE	-27.59
Energy contribution	-28.90
Covariance contribution	1.31
Combinations/Pair	1.13
Mean z-score	-1.79
Structure conservation index	0.75
SVM decision value	0.53
SVM RNA-class probability	0.772603
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13687518 119 + 27905053
CCAGUGCCAUAUUGAGCGCAUAAAAGGCUGCUAAACAGCGUGGCUCAGAUUACCAGGCGAUUCCUGAAUGGGUGGGUGAGUGUGGAUGGAGUGUGGAUGGAGAACCAAGUGGCAGUGGA
(((.((((((.((((((.(((.....((((.....)))))))))))))....(((.((....(((........)))...)).)))............(((....))).)))))).))). ( -38.50)
>DroSec_CAF1 14651 112 + 1
CCAGUGCCAUAUUGAGCCCAUAAAAGGCUGCUAAACAGCGUGGCUCAGAUUACCAGGCGGUUCCUGGAUGGAUGGGUGAGUUU-------AUGUGGAUGGAGAACCAAGUGGUAGUGGA
(((.((((((......((((((((..((((.....)))).(.(((((.....(((((.....))))).....))))).).)))-------))).)).(((....))).)))))).))). ( -38.40)
>DroSim_CAF1 14826 112 + 1
CCAGUGCCAUAUUGAGCGCAUAAAAGGCUGCUAAACAGCGUGGCUCAGAUUACCAGGCGGUUCCUGGUUGGGUGGGUGAGUGU-------GUGUGGAUGGAGAACCAAGUGGUAGUGGA
(((.((((((.....(((((((....((((.....)))).(.(((((..(.((((((.....)))))).)..))))).).)))-------))))...(((....))).)))))).))). ( -41.20)
>DroEre_CAF1 9358 93 + 1
CCAGUGCCAUAUUGAGCGCAUAAAAGGCUGCUAAACAGCGCGGCUCAGAUUACCAGGCGGUUCCUGGAUGGAUGGGUGGGU--------------------GAACGAA------GUGGG
......((((.(((..(((.......((((.....)))).(.(((((.....(((((.....))))).....))))).)))--------------------)..))).------)))). ( -29.30)
>consensus
CCAGUGCCAUAUUGAGCGCAUAAAAGGCUGCUAAACAGCGUGGCUCAGAUUACCAGGCGGUUCCUGGAUGGAUGGGUGAGUGU_______GUGUGGAUGGAGAACCAAGUGGUAGUGGA
(((.((((((.((((((.(((.....((((.....))))))))))))).(((((...(.(((....))).)...))))).............................)))))).))). (-27.59 = -28.90 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	13,687,518 – 13,687,637
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	83.84
Mean single sequence MFE	-25.94
Consensus MFE	-21.30
Energy contribution	-20.93
Covariance contribution	-0.37
Combinations/Pair	1.09
Mean z-score	-1.72
Structure conservation index	0.82
SVM decision value	0.52
SVM RNA-class probability	0.768937
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13687518 119 - 27905053
UCCACUGCCACUUGGUUCUCCAUCCACACUCCAUCCACACUCACCCACCCAUUCAGGAAUCGCCUGGUAAUCUGAGCCACGCUGUUUAGCAGCCUUUUAUGCGCUCAAUAUGGCACUGG
.(((.(((((..(((....)))..............................(((((.....))))).....(((((((.((((.....))))......)).)))))...))))).))) ( -27.40)
>DroSec_CAF1 14651 112 - 1
UCCACUACCACUUGGUUCUCCAUCCACAU-------AAACUCACCCAUCCAUCCAGGAACCGCCUGGUAAUCUGAGCCACGCUGUUUAGCAGCCUUUUAUGGGCUCAAUAUGGCACUGG
.(((.(((((..(((((((..........-------...................)))))))..)))))...((((((..((((.....))))(......)))))))...)))...... ( -27.85)
>DroSim_CAF1 14826 112 - 1
UCCACUACCACUUGGUUCUCCAUCCACAC-------ACACUCACCCACCCAACCAGGAACCGCCUGGUAAUCUGAGCCACGCUGUUUAGCAGCCUUUUAUGCGCUCAAUAUGGCACUGG
............(((....))).......-------........(((.(((((((((.....))))))....(((((((.((((.....))))......)).)))))...)))...))) ( -25.30)
>DroEre_CAF1 9358 93 - 1
CCCAC------UUCGUUC--------------------ACCCACCCAUCCAUCCAGGAACCGCCUGGUAAUCUGAGCCGCGCUGUUUAGCAGCCUUUUAUGCGCUCAAUAUGGCACUGG
.....------.......--------------------......(((.(((((((((.....))))).....(((((.((((((.....)))).......)))))))..))))...))) ( -23.21)
>consensus
UCCACUACCACUUGGUUCUCCAUCCACAC_______ACACUCACCCACCCAUCCAGGAACCGCCUGGUAAUCUGAGCCACGCUGUUUAGCAGCCUUUUAUGCGCUCAAUAUGGCACUGG
............................................(((.(((.(((((.....))))).....(((((((.((((.....))))......)).)))))...)))...))) (-21.30 = -20.93 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:47 2006