Locus 1057

Sequence ID	X_DroMel_CAF1
Location	3,089,800 – 3,089,902
Length	102
Max. P	0.853139

overview

Window 8

Location	3,089,800 – 3,089,902
Length	102
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	83.21
Mean single sequence MFE	-20.91
Consensus MFE	-12.74
Energy contribution	-12.50
Covariance contribution	-0.24
Combinations/Pair	1.20
Mean z-score	-1.96
Structure conservation index	0.61
SVM decision value	0.15
SVM RNA-class probability	0.609763
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3089800 102 + 22224390
UGUUGAAGGGUAUUGAAAAUUUCCAAAAACCAAAGGAGGUCAGAGGAAAUUUCUCUAUCCAUCUGCUAUCCACCCACUUCCGUUCCCC-------CGAUUUUGCCCUUC
....(((((((((((........)))........(((((((((((((..........))).))))..........)))))).......-------......)))))))) ( -22.20)
>DroSec_CAF1 52018 100 + 1
----GCAGGGUAUUGAAAAUUUGCCAAAACCAAAGGAGGUCAGAGGAAAUUUCUCUAUCCAUCUCCAAUCCU-CCACUUCCGUUUCCCC----UCCCACUUUGCCCCUC
----...(((((..(....((((.......))))((((((..(((((.....................))))-).))))))........----.....)..)))))... ( -20.00)
>DroSim_CAF1 47849 100 + 1
----GCAGGGUAUUGAAAAUUUGCCAAAACCAAAGGAGGUCAGAGGAAAUUUCUCUAUCCAUCUCCAAUCCU-CCACUUCCGUUUCCCC----UCCCACUUUGCCCCUC
----...(((((..(....((((.......))))((((((..(((((.....................))))-).))))))........----.....)..)))))... ( -20.00)
>DroEre_CAF1 53458 101 + 1
UGUUGAAGGGGAUUGAAAAUUUUCGAAAACCAACGCAGGUCAGAGGAUAUUUCUCUAUCCAUCUCCUAUCCU-CCACUUCCGUUCCC-------CCUACUUUUCUCCCC
......(((((.(((((....))))).....((((.((((..(((((((.................))))))-).)))).)))).))-------)))............ ( -22.63)
>DroYak_CAF1 54633 108 + 1
UGUUGAAGGGUAUUGAAAAUUUCCGAAAACCAAAGGAGGUCAGAGGAAAUUUAUCUACCCAUCUCCUAUUCU-CCACUUUCGUGCCCCCAUUUCCCUAUUUUACCCCUC
....((.(((((..((((((((((....(((......)))....)))))))).))))))).)).........-.(((....)))......................... ( -19.70)
>consensus
UGUUGAAGGGUAUUGAAAAUUUCCCAAAACCAAAGGAGGUCAGAGGAAAUUUCUCUAUCCAUCUCCUAUCCU_CCACUUCCGUUCCCCC_____CCCACUUUGCCCCUC
.......(((((..(...................((((((.((((((...))))))....)))))).........((....))...............)..)))))... (-12.74 = -12.50 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	3,089,800 – 3,089,902
Length	102
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	83.21
Mean single sequence MFE	-30.05
Consensus MFE	-21.26
Energy contribution	-22.10
Covariance contribution	0.84
Combinations/Pair	1.14
Mean z-score	-2.07
Structure conservation index	0.71
SVM decision value	0.80
SVM RNA-class probability	0.853139
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3089800 102 - 22224390
GAAGGGCAAAAUCG-------GGGGAACGGAAGUGGGUGGAUAGCAGAUGGAUAGAGAAAUUUCCUCUGACCUCCUUUGGUUUUUGGAAAUUUUCAAUACCCUUCAACA
((((((.(((((((-------(((((((....))....((....((((.(((..((....))))))))).))))))))))))))((((....))))...)))))).... ( -31.80)
>DroSec_CAF1 52018 100 - 1
GAGGGGCAAAGUGGGA----GGGGAAACGGAAGUGG-AGGAUUGGAGAUGGAUAGAGAAAUUUCCUCUGACCUCCUUUGGUUUUGGCAAAUUUUCAAUACCCUGC----
.((((......((..(----(.(....)....((.(-((.((..(((..((.(((((.......))))).))..)))..))))).))...))..))...))))..---- ( -27.60)
>DroSim_CAF1 47849 100 - 1
GAGGGGCAAAGUGGGA----GGGGAAACGGAAGUGG-AGGAUUGGAGAUGGAUAGAGAAAUUUCCUCUGACCUCCUUUGGUUUUGGCAAAUUUUCAAUACCCUGC----
.((((......((..(----(.(....)....((.(-((.((..(((..((.(((((.......))))).))..)))..))))).))...))..))...))))..---- ( -27.60)
>DroEre_CAF1 53458 101 - 1
GGGGAGAAAAGUAGG-------GGGAACGGAAGUGG-AGGAUAGGAGAUGGAUAGAGAAAUAUCCUCUGACCUGCGUUGGUUUUCGAAAAUUUUCAAUCCCCUUCAACA
(((((((((((((((-------....((....))((-((((((.................))))))))..))))).(((.....)))...)))))..)))))....... ( -29.53)
>DroYak_CAF1 54633 108 - 1
GAGGGGUAAAAUAGGGAAAUGGGGGCACGAAAGUGG-AGAAUAGGAGAUGGGUAGAUAAAUUUCCUCUGACCUCCUUUGGUUUUCGGAAAUUUUCAAUACCCUUCAACA
((((((((......((((((.....(((....)))(-((((((((((.(.((..((......))..)).).)))))...))))))....))))))..)))))))).... ( -33.70)
>consensus
GAGGGGCAAAGUAGG_____GGGGGAACGGAAGUGG_AGGAUAGGAGAUGGAUAGAGAAAUUUCCUCUGACCUCCUUUGGUUUUCGCAAAUUUUCAAUACCCUUCAACA
((((((................(....)((((((...(((((..(((..((.(((((.......))))).))..)))..))))).....))))))....)))))).... (-21.26 = -22.10 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:34 2006