Locus 5062

Sequence ID	3R_DroMel_CAF1
Location	13,334,733 – 13,334,914
Length	181
Max. P	0.929613

overview

Window 6

Location	13,334,733 – 13,334,824
Length	91
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	91.48
Mean single sequence MFE	-13.66
Consensus MFE	-11.12
Energy contribution	-11.52
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.81
SVM decision value	1.20
SVM RNA-class probability	0.929613
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13334733 91 - 27905053
ACUCAGUGCCGCA---UCCACAGCCCAAUCUCAAUCCCAACCCUCUGGAAAAAGUUUUCGUGUACUGGCAAACACUUUUUCCUUACACAACCCC
.....(((..((.---......))......................(((((((((.....(((....)))...)))))))))...)))...... ( -13.40)
>DroSec_CAF1 87273 91 - 1
ACUCAGUGGCGCA---UCCACAGCCCAAUCUCAAUCCCAACCCUCUGGAAAAAGUUUUCGUGUACUGGCAAACACUUUUUCCUUACACAACCCC
.....((((....---.)))).........................(((((((((.....(((....)))...)))))))))............ ( -15.20)
>DroSim_CAF1 91543 91 - 1
ACUCAGUGGCGCA---UCCACAGCCCAAUCUCAAUCCCAACCCUCUGGAAAAAGUUUUCGUGUACUGGCAAACACUUUUUCCUUACACAACCCC
.....((((....---.)))).........................(((((((((.....(((....)))...)))))))))............ ( -15.20)
>DroEre_CAF1 93599 85 - 1
ACUCAGAGCCGCA---UCCACAGCCCGA------UCCCAACUCUCUGGAAAAAGUUUUCGUGUACUGGCAAACACUUUUUCCUUACACAACCCC
....((((..(.(---((........))------).)...))))..(((((((((.....(((....)))...)))))))))............ ( -12.70)
>DroYak_CAF1 104894 88 - 1
ACUCAGUACCGCAUCAUCCACAGCCCAG------UCCCAACCCUCUGGAAAAAGUUUUCGUGUACUGGCAAACACUUUUUCCCUACACAACCCC
..((((((((((..........))((((------..........))))...........).))))))).......................... ( -11.80)
>consensus
ACUCAGUGCCGCA___UCCACAGCCCAAUCUCAAUCCCAACCCUCUGGAAAAAGUUUUCGUGUACUGGCAAACACUUUUUCCUUACACAACCCC
.....(((..((..........))......................(((((((((.....(((....)))...)))))))))...)))...... (-11.12 = -11.52 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	13,334,824 – 13,334,914
Length	90
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	84.12
Mean single sequence MFE	-17.73
Consensus MFE	-13.22
Energy contribution	-13.38
Covariance contribution	0.17
Combinations/Pair	1.08
Mean z-score	-2.05
Structure conservation index	0.75
SVM decision value	0.23
SVM RNA-class probability	0.646200
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13334824 90 - 27905053
AAUGCCAUCAUCAUCGGCACCACCGCCCCCCACUUGCGGUCUGCACCACUCAACAAGGAAAGCAGACUUUA---CACCCACAUCCGCAUCCAC
.((((..........(((......)))..........(((((((.((.........))...)))))))...---...........)))).... ( -16.80)
>DroSec_CAF1 87364 90 - 1
AAUGCCAUCAUCAUCGGCACCACCGCCCCCCAGUUGCGGUCUGCACCACUCAACAAGGAAAGCAGACGUUA---CACCCACAUCCGCACCCAC
..(((..........(((......))).....((.(((.(((((.((.........))...)))))))).)---)..........)))..... ( -17.60)
>DroSim_CAF1 91634 89 - 1
AAUGCCAUCAUCAUCGGCACCACCGCC-CCCAGUUGCGGUCUGCACCACUCAACAAGGAAAGCAGACUUUA---CCCCCACAUCCGCACCCAC
..(((..........(((......)))-....((...(((((((.((.........))...)))))))..)---)..........)))..... ( -16.40)
>DroEre_CAF1 93684 78 - 1
AAUGCCAUCAUCAUCGGCACCACCGCCCCUCAGUUGCGGUCUGCACCACUCAACAAGGAAAGCAGACCCUA---CACC------------CAC
..((((.........)))).............((.(.(((((((.((.........))...)))))))).)---)...------------... ( -17.90)
>DroYak_CAF1 104982 90 - 1
AAUGCCAUCAUCAUCGGCACCACAGCCCAUCAGUUGGGGUCUGCACCACUCAACAAGGAAAGCAGACCUUA---CACCCACAUCCGCACCCAC
..(((..........(((......))).....((.(((((((((.((.........))...))))))))))---)..........)))..... ( -21.30)
>DroAna_CAF1 106543 85 - 1
UCUGCCAUCAUCAUCGGCACCAUCGCCCCCAGUUUGCGGUCUGCACCACUCAACAAGCAGUGCUGACUUUCAGCCACCCACAUCC--------
.((((..........(((......)))....(((.(.(((....))).)..)))..)))).((((.....))))...........-------- ( -16.40)
>consensus
AAUGCCAUCAUCAUCGGCACCACCGCCCCCCAGUUGCGGUCUGCACCACUCAACAAGGAAAGCAGACUUUA___CACCCACAUCCGCACCCAC
..((((.........))))..................(((((((....((.....))....)))))))......................... (-13.22 = -13.38 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:17 2006