Locus 5969

Sequence ID	2R_DroMel_CAF1
Location	18,801,208 – 18,801,304
Length	96
Max. P	0.980709

overview

Window 3

Location	18,801,208 – 18,801,304
Length	96
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	74.33
Mean single sequence MFE	-37.92
Consensus MFE	-18.28
Energy contribution	-20.68
Covariance contribution	2.40
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.48
SVM decision value	1.87
SVM RNA-class probability	0.980709
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18801208 96 + 20766785
AGCGCCAC-----------AGGU--CCCCGCUCCCCAGCUCCAGCUGGU-AGCUCCCCAUCUUCCCGUUUGCAUGGGUUAAGGUUAACCCACUGCGUCCUGGCCGCUCCA
((((.(.(-----------(((.--(...(((..(((((....))))).-))).................((((((((((....))))))).)))).))))).))))... ( -34.60)
>DroSec_CAF1 20666 95 + 1
AGCGCCAC-----------AGG---CCCCGCUGCCCAGCUCCAGCUGGG-AGCUCCCCAUCUUCCCGGCUGCAUGGGUUAAGGUUAACCCACUGCGUCCUGGCCGCUCCA
(((((((.-----------.((---....(((.((((((....))))))-)))...))........((.(((((((((((....))))))).)))).))))).))))... ( -40.60)
>DroSim_CAF1 20632 95 + 1
AGCGCCAC-----------AGG---CCCCGCUGCCCAGCUCCAGCUGGG-AGCUCCCCAUCUUCCCGGCUGCAUGGGUUAAGGUUAACCCACUGCGUCCUGGCCGCUCCA
(((((((.-----------.((---....(((.((((((....))))))-)))...))........((.(((((((((((....))))))).)))).))))).))))... ( -40.60)
>DroYak_CAF1 20989 91 + 1
AGCGCCAA-----------UGG---CCCCGCUCCCC-----CUGCUGUCCCCCUGCCCCGCUGCCCGGCUUCAUGGGUUAAGGUUAACCCACUGCGUCCUGGCCGGUCCA
((((.((.-----------.((---..(.((.....-----..)).)..))..))...))))..((((((.(((((((((....))))))).))......)))))).... ( -25.90)
>DroAna_CAF1 7901 95 + 1
AGCGCCCUGGAAGGCAGUCAGGCAGUCAGGCUGCCUUGCUGC----------CUUGCUGGCUUGCUGGCUUCAUGGGUUAAGGUUAACCCACUGCGUCCAGGCCG-----
.(((((..(.((((((((.((((((.....)))))).)))))----------))).).)))...((((...(((((((((....))))))).))...))))))..----- ( -47.90)
>consensus
AGCGCCAC___________AGG___CCCCGCUGCCCAGCUCCAGCUGGG_AGCUCCCCAUCUUCCCGGCUGCAUGGGUUAAGGUUAACCCACUGCGUCCUGGCCGCUCCA
.(.(((............................(((((....)))))..................((.(((((((((((....))))))).)))).)).))))...... (-18.28 = -20.68 +   2.40)

alignment

secondary structure

dotplot

Window 4

Location	18,801,208 – 18,801,304
Length	96
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	74.33
Mean single sequence MFE	-41.26
Consensus MFE	-20.10
Energy contribution	-21.98
Covariance contribution	1.88
Combinations/Pair	1.05
Mean z-score	-1.70
Structure conservation index	0.49
SVM decision value	-0.05
SVM RNA-class probability	0.506349
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18801208 96 - 20766785
UGGAGCGGCCAGGACGCAGUGGGUUAACCUUAACCCAUGCAAACGGGAAGAUGGGGAGCU-ACCAGCUGGAGCUGGGGAGCGGGG--ACCU-----------GUGGCGCU
...((((.(((((..(((.(((((((....)))))))))).................(((-.(((((....)))))..)))....--.)))-----------).).)))) ( -39.70)
>DroSec_CAF1 20666 95 - 1
UGGAGCGGCCAGGACGCAGUGGGUUAACCUUAACCCAUGCAGCCGGGAAGAUGGGGAGCU-CCCAGCUGGAGCUGGGCAGCGGGG---CCU-----------GUGGCGCU
...((((.(((((.(((.((((((((....))))))))...(((.((.((.((((.....-)))).))....)).))).)))...---)))-----------).).)))) ( -44.40)
>DroSim_CAF1 20632 95 - 1
UGGAGCGGCCAGGACGCAGUGGGUUAACCUUAACCCAUGCAGCCGGGAAGAUGGGGAGCU-CCCAGCUGGAGCUGGGCAGCGGGG---CCU-----------GUGGCGCU
...((((.(((((.(((.((((((((....))))))))...(((.((.((.((((.....-)))).))....)).))).)))...---)))-----------).).)))) ( -44.40)
>DroYak_CAF1 20989 91 - 1
UGGACCGGCCAGGACGCAGUGGGUUAACCUUAACCCAUGAAGCCGGGCAGCGGGGCAGGGGGACAGCAG-----GGGGAGCGGGG---CCA-----------UUGGCGCU
((..((((((.((.(...((((((((....))))))))...))).)))..)))..)).(....).((..-----.....))((.(---((.-----------..))).)) ( -31.10)
>DroAna_CAF1 7901 95 - 1
-----CGGCCUGGACGCAGUGGGUUAACCUUAACCCAUGAAGCCAGCAAGCCAGCAAG----------GCAGCAAGGCAGCCUGACUGCCUGACUGCCUUCCAGGGCGCU
-----((.((((((.((.((((((((....))))))))...))..((......)).((----------((((..((((((.....))))))..)))))))))))).)).. ( -46.70)
>consensus
UGGAGCGGCCAGGACGCAGUGGGUUAACCUUAACCCAUGCAGCCGGGAAGAUGGGGAGCU_CCCAGCUGGAGCUGGGCAGCGGGG___CCU___________GUGGCGCU
.......((((...(((.((((((((....))))))))........................(((((....)))))...)))((....)).............))))... (-20.10 = -21.98 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:17 2006