Locus 5423

Sequence ID	3L_DroMel_CAF1
Location	14,862,926 – 14,863,056
Length	130
Max. P	0.705526

overview

Window 4

Location	14,862,926 – 14,863,044
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	86.04
Mean single sequence MFE	-25.30
Consensus MFE	-21.08
Energy contribution	-21.70
Covariance contribution	0.62
Combinations/Pair	1.04
Mean z-score	-1.55
Structure conservation index	0.83
SVM decision value	0.27
SVM RNA-class probability	0.659744
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14862926 118 - 23771897
AUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAACGCACAUGCACUGCAAAACAAGAAGCGUUCGACAGAUUAAUCAAAUAAAAUAAAUAAAUAG
.(((((((..((....))..)))(((((.........))))))))).....(((((((((.....................)))))).)))........................... ( -24.60)
>DroSec_CAF1 44997 116 - 1
AUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAGCGCACAUGCACUGCA--ACAAAAAGCGUUCGACAGAUUAAGCAAAUAAAAUAAAUAAAUGG
.(((((((..((....))..)))(((((.........))))))))).(((((((((((((...(((...)))--.......)))))).)))...)))).................... ( -25.40)
>DroSim_CAF1 40177 116 - 1
AUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAACGCACAUGCACUGCA--GCAAAAAGCGUUCGACAGAUUAAGCAAAUAAAAUAAAUAAAUAG
.(((((((..((....))..)))(((((.........))))))))).(((((((((((((...(((......--)))....)))))).)))...)))).................... ( -29.00)
>DroEre_CAF1 41305 98 - 1
AUGGCUGGAAGGCAAACCGACCACAUGCAGCCCAACAGCUUGGCCAACUUAUGUGAACGCACAUGCACUGAA--ACAAAAGGCGCUAGCCAGAUUU-----------------UA-AG
.(((((((...((........((((((.((.((((....))))....))))))))...((....))......--.......)).))))))).....-----------------..-.. ( -22.20)
>consensus
AUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAACGCACAUGCACUGCA__ACAAAAAGCGUUCGACAGAUUAAGCAAAUAAAAUAAAUAAAUAG
.(((((((..((....))..)))(((((.........))))))))).....(((((((((.....................))))))).))........................... (-21.08 = -21.70 +   0.62)

alignment

secondary structure

dotplot

Window 5

Location	14,862,966 – 14,863,056
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	77.39
Mean single sequence MFE	-23.37
Consensus MFE	-16.20
Energy contribution	-16.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.69
SVM decision value	0.34
SVM RNA-class probability	0.696700
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14862966 90 + 23771897
UUGUUUUGCAGUGCAUGUGCGUUCACAUAAGUUGGCCAAGCUGUUGGGCUGCUUGUGGUCGGUUUGCCUUCCAGCCAUAUUCCCAUCCAU
.......(((((.((...((.....((.....)).....))...)).))))).((((((.((........)).))))))........... ( -22.50)
>DroPse_CAF1 93988 69 + 1
---------------------UACAUAUAAGUUGGCCAAGCUGCUGGCCUGCUUGUGGUCGGCUUGCCUGCCAGCCAUAUACCCAUCCAU
---------------------.....((((((.(((((......))))).))))))(((.(((......))).))).............. ( -24.10)
>DroSec_CAF1 45037 88 + 1
UUGU--UGCAGUGCAUGUGCGCUCACAUAAGUUGGCCAAGCUGUUGGGCUGCUUGUGGUCGGUUUGCCUUCCAGCCAUAUACCCAUCCAU
....--.(((((.((...(((((.((....)).)))...))...)).))))).((((((.((........)).))))))........... ( -23.90)
>DroSim_CAF1 40217 88 + 1
UUGC--UGCAGUGCAUGUGCGUUCACAUAAGUUGGCCAAGCUGUUGGGCUGCUUGUGGUCGGUUUGCCUUCCAGCCAUAUACCCAUCCAU
..((--((.((.(((....((....(((((((.(.((((....)))).).)))))))..))...)))))..))))............... ( -23.20)
>DroAna_CAF1 32964 76 + 1
--AU--UGUAGUCUAAGUGC----------UUUGGCCAAGCUGUUGGCCUGCUUGUGGUCGGGUAGCCUUCCAGCCAUAUACCCAUCCAU
--..--............((----------...((((((....)))))).))..((((..(((((((......))....)))))..)))) ( -22.40)
>DroPer_CAF1 91429 69 + 1
---------------------UACAUAUAAGUUGGCCAAGCUGCUGGCCUGCUUGUGGUCGGCUUGCCUGCCAGCCAUAUACCCAUCCAU
---------------------.....((((((.(((((......))))).))))))(((.(((......))).))).............. ( -24.10)
>consensus
__GU__UGCAGUGCAUGUGC_UUCACAUAAGUUGGCCAAGCUGUUGGCCUGCUUGUGGUCGGUUUGCCUUCCAGCCAUAUACCCAUCCAU
................................(((((((((.........)))))(((..((....))..)))))))............. (-16.20 = -16.20 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	14,862,966 – 14,863,056
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	77.39
Mean single sequence MFE	-21.82
Consensus MFE	-16.33
Energy contribution	-16.33
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.06
Structure conservation index	0.75
SVM decision value	0.36
SVM RNA-class probability	0.705526
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14862966 90 - 23771897
AUGGAUGGGAAUAUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAACGCACAUGCACUGCAAAACAA
.............(((((((..((....))..)))(((((.........)))))))))...((((((....))))))............. ( -20.30)
>DroPse_CAF1 93988 69 - 1
AUGGAUGGGUAUAUGGCUGGCAGGCAAGCCGACCACAAGCAGGCCAGCAGCUUGGCCAACUUAUAUGUA---------------------
....((((((...(((.((((......)))).)))......((((((....)))))).)))))).....--------------------- ( -21.40)
>DroSec_CAF1 45037 88 - 1
AUGGAUGGGUAUAUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAGCGCACAUGCACUGCA--ACAA
....((((((...(((((((..((....))..)))(((((.........)))))))))))))))((.((.((....)).)))).--.... ( -22.10)
>DroSim_CAF1 40217 88 - 1
AUGGAUGGGUAUAUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAACGCACAUGCACUGCA--GCAA
....((((((...(((((((..((....))..)))(((((.........)))))))))))))))(((....))).(((......--))). ( -22.50)
>DroAna_CAF1 32964 76 - 1
AUGGAUGGGUAUAUGGCUGGAAGGCUACCCGACCACAAGCAGGCCAACAGCUUGGCCAAA----------GCACUUAGACUACA--AU--
.(((.(((((....((((....))))))))).)))...((.((((((....))))))...----------))............--..-- ( -23.20)
>DroPer_CAF1 91429 69 - 1
AUGGAUGGGUAUAUGGCUGGCAGGCAAGCCGACCACAAGCAGGCCAGCAGCUUGGCCAACUUAUAUGUA---------------------
....((((((...(((.((((......)))).)))......((((((....)))))).)))))).....--------------------- ( -21.40)
>consensus
AUGGAUGGGUAUAUGGCUGGAAGGCAAACCGACCACAAGCAGCCCAACAGCUUGGCCAACUUAUGUGAA_GCACAUGCACUGCA__AC__
.............(((((((..((....))..)))(((((.........)))))))))................................ (-16.33 = -16.33 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:02 2006