Locus 6296

Sequence ID	2R_DroMel_CAF1
Location	19,747,159 – 19,747,291
Length	132
Max. P	0.939055

overview

Window 4

Location	19,747,159 – 19,747,259
Length	100
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	83.66
Mean single sequence MFE	-43.67
Consensus MFE	-33.49
Energy contribution	-33.42
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.96
Structure conservation index	0.77
SVM decision value	0.87
SVM RNA-class probability	0.869989
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19747159 100 + 20766785
GGUC--ACGC-------CCACCGCCUCCGCUGUCAAUCAACAGGGGGUGGGAGCAACAACGGGAGUG-GGGCGUGGCAGCAAUUUGUCCACGCCAAAGAGCCAGGUGUUU
((((--((.(-------((.(((((.((.((((......)))))))))))..(......)))).)))-.((((((((((....))).))))))).....)))........ ( -41.30)
>DroSec_CAF1 4 88 + 1
GGCU--GCGC-------CCACCGCCUCCGCUGUCAAUCAACAGGGGGCGGG------------AGCG-GGGAGUGGCAGCAAUUUGUCCACGCCAAAGAGCCAGGUGUUU
.(((--((((-------((.((((..(((((.((........)).))))).------------.)))-))).)).))))).........(((((.........))))).. ( -39.10)
>DroSim_CAF1 2476 88 + 1
GGCC--ACGC-------CCACCGCCUCCGCUGUCAAUCAACAGGGGGCGGG------------AGCG-GGGCGUGGCAGCAAUUUGUCCACGCCAAAGAGCCAGGUGUUU
.(((--((((-------((.(((((.((.((((......))))))))))).------------....-)))))))))............(((((.........))))).. ( -43.60)
>DroEre_CAF1 5 104 + 1
CGCCCACCGCCCGCAGCCCACCGCCUCCGCUGUCAAUCAAGAGGGGGCGGGAGG------GGGAGCGAGGGCGUGGCAGCAAUUUGUCCACGCCAAAGAGCCAGGUGUUU
....((((...(((..(((.((((((((.((........)).))))))))...)------))..)))..((((((((((....))).))))))).........))))... ( -50.70)
>consensus
GGCC__ACGC_______CCACCGCCUCCGCUGUCAAUCAACAGGGGGCGGG____________AGCG_GGGCGUGGCAGCAAUUUGUCCACGCCAAAGAGCCAGGUGUUU
(((....(((..........((((((((..((.....))...))))))))..............)))..((((((((((....))).))))))).....)))........ (-33.49 = -33.42 +  -0.06)

alignment

secondary structure

dotplot

Window 5

Location	19,747,159 – 19,747,259
Length	100
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	83.66
Mean single sequence MFE	-43.75
Consensus MFE	-30.99
Energy contribution	-31.30
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.33
Structure conservation index	0.71
SVM decision value	1.29
SVM RNA-class probability	0.938524
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19747159 100 - 20766785
AAACACCUGGCUCUUUGGCGUGGACAAAUUGCUGCCACGCCC-CACUCCCGUUGUUGCUCCCACCCCCUGUUGAUUGACAGCGGAGGCGGUGG-------GCGU--GACC
........((......(((((((.((......))))))))).-.....))...((..(.((((((((((((((.....)))))).)).)))))-------).).--.)). ( -43.40)
>DroSec_CAF1 4 88 - 1
AAACACCUGGCUCUUUGGCGUGGACAAAUUGCUGCCACUCCC-CGCU------------CCCGCCCCCUGUUGAUUGACAGCGGAGGCGGUGG-------GCGC--AGCC
........((((....((.((((.((......)))))).)).-((((------------(((((((((((((....))))).)).))))).))-------))).--)))) ( -39.70)
>DroSim_CAF1 2476 88 - 1
AAACACCUGGCUCUUUGGCGUGGACAAAUUGCUGCCACGCCC-CGCU------------CCCGCCCCCUGUUGAUUGACAGCGGAGGCGGUGG-------GCGU--GGCC
........((((....(((((((.((......))))))))).-((((------------(((((((((((((....))))).)).))))).))-------))).--)))) ( -45.60)
>DroEre_CAF1 5 104 - 1
AAACACCUGGCUCUUUGGCGUGGACAAAUUGCUGCCACGCCCUCGCUCCC------CCUCCCGCCCCCUCUUGAUUGACAGCGGAGGCGGUGGGCUGCGGGCGGUGGGCG
...((((.........(((((((.((......)))))))))(((((..((------(...(((((.((.((........)).)).))))).)))..))))).)))).... ( -46.30)
>consensus
AAACACCUGGCUCUUUGGCGUGGACAAAUUGCUGCCACGCCC_CGCU____________CCCGCCCCCUGUUGAUUGACAGCGGAGGCGGUGG_______GCGU__GGCC
.........((.....(((((((.((......)))))))))...................(((((((((((((.....)))))).)).))))).......))........ (-30.99 = -31.30 +   0.31)

alignment

secondary structure

dotplot

Window 6

Location	19,747,190 – 19,747,291
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.51
Mean single sequence MFE	-35.07
Consensus MFE	-15.29
Energy contribution	-14.93
Covariance contribution	-0.36
Combinations/Pair	1.30
Mean z-score	-2.24
Structure conservation index	0.44
SVM decision value	1.27
SVM RNA-class probability	0.939055
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19747190 101 - 20766785
CAAACUUUGCCGCGGGC-----CAAGGAGA---CAGGCUCA--AACACCUGGCUCUUUGGCGUGGACAAAUU--GCU-GCCAC-----GCCC-CACUCCCGUUGUUGCUCCCACCCCCUG
........((.(((((.-----.((((((.---((((....--....)))).))))))(((((((.((....--..)-)))))-----))).-....))))).))............... ( -34.10)
>DroPse_CAF1 8183 108 - 1
AAAACUUUGCCGGGGGCAGCAGCAAAGGCA---GAGGCCAAACAACAUCUGGGUCUUGGACCAGGACAAACACUCCUCUCCACUGCGUGCCC-CACC--UGUC------CGUGGCUCCAG
........((((.((((((..(((..((.(---(((((((.........)))((((((...)))))).......)))))))..)))(((...-))))--))))------).))))..... ( -37.20)
>DroSec_CAF1 35 89 - 1
CAAACUUUGCCGCGGGC-----CAAGGAGA---CAGGCUCA--AACACCUGGCUCUUUGGCGUGGACAAAUU--GCU-GCCAC-----UCCC-CGCU------------CCCGCCCCCUG
...........((((((-----(((((((.---((((....--....)))).)))))))))((((.((....--..)-)))))-----...)-))).------------........... ( -34.70)
>DroSim_CAF1 2507 89 - 1
CAAACUUUGCCGCGGGC-----CAAGGAGA---CAGGCUCA--AACACCUGGCUCUUUGGCGUGGACAAAUU--GCU-GCCAC-----GCCC-CGCU------------CCCGCCCCCUG
...........(((((.-----(((((((.---((((....--....)))).)))))))((((((.((....--..)-)))))-----))))-))).------------........... ( -35.40)
>DroEre_CAF1 45 99 - 1
CAAACUUUGCCGCGGGC-----CAAGGAGCCGCCGGGCUCA--AACACCUGGCUCUUUGGCGUGGACAAAUU--GCU-GCCAC-----GCCCUCGCUCCC------CCUCCCGCCCCCUC
...........(((((.-----...(((((.((((((....--....)))))).....(((((((.((....--..)-)))))-----)))...))))).------...)))))...... ( -43.70)
>DroYak_CAF1 2520 77 - 1
CAAACUUUGCCGCGGGC-----CACGAAGA---CGGGCUCA--AACACCUGGCUCUUUGGCGUGGACAAAUU--GCU-GCCAC-----GCC-------------------------CCUG
........((((.((((-----(.((....---))))))).--......)))).....(((((((.((....--..)-)))))-----)))-------------------------.... ( -25.30)
>consensus
CAAACUUUGCCGCGGGC_____CAAGGAGA___CAGGCUCA__AACACCUGGCUCUUUGGCGUGGACAAAUU__GCU_GCCAC_____GCCC_CGCU____________CCCGCCCCCUG
.....(((((((((........(((((((....((((..........)))).))))))).))))).)))).................................................. (-15.29 = -14.93 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:39 2006