Locus 5080

Sequence ID	2L_DroMel_CAF1
Location	14,508,718 – 14,508,818
Length	100
Max. P	0.997374

overview

Window 6

Location	14,508,718 – 14,508,818
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.89
Mean single sequence MFE	-33.50
Consensus MFE	-30.82
Energy contribution	-31.46
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	0.92
SVM decision value	2.85
SVM RNA-class probability	0.997374
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14508718 100 + 22407834
CUGGGGAUCGGAUCGGUCCUGGAAUUGUAAAAUUGGGGUGUAACCCACUGUCGGCUUACACACUCAAGUCAAGCGACCAACGCCAUCCCCAU-C-------------------AACCGAA
.(((((((.((...((((((.((.........(((((((((((.((......)).)))))).))))).)).)).))))....))))))))).-.-------------------....... ( -34.90)
>DroSec_CAF1 40350 100 + 1
CUGGGGAUCGGAUCGGUCCUGGAAUUGUAAAAUUGGGGUGUAACCCACUGUCGGCUUACACACUCAAGUCAAGCGACCAACGCCAUCCCCAU-C-------------------AACCGAA
.(((((((.((...((((((.((.........(((((((((((.((......)).)))))).))))).)).)).))))....))))))))).-.-------------------....... ( -34.90)
>DroSim_CAF1 25053 100 + 1
CUGGGGAUCGGAUCGGUCCUGGAAUUGUAAAAUUGGGGUGUAACCCACUGUCGGCUUACACACUCAAGUCAAGCGACCAACGCCAUCCCCAU-G-------------------AACCGAA
.(((((((.((...((((((.((.........(((((((((((.((......)).)))))).))))).)).)).))))....))))))))).-.-------------------....... ( -34.90)
>DroEre_CAF1 33831 99 + 1
CUGG-CAUCGGAUCGGUCCUGGAAUUGUAAAAUUGGGGUGUAACCCACUGUCGGCUUACACACUCAAGUCAAGCGACCAACGCCAUCCCCAA-C-------------------AGCUGAA
(((.-....((((.(((..(((..((((....(((((((((((.((......)).)))))).))))).....)))))))..)))))))....-)-------------------))..... ( -28.30)
>DroYak_CAF1 29778 120 + 1
CUGGGGAUCGCAUCGGUCCUGGAAUUGUAAAAUUGGGGUGUAACCCACUGUCGGCUUACACACUCGAGUCAAGCGACCAACGCCAUCCCCCAUCAGCCUCACCAACAUAACCUAACUGAA
..((((((.((...((((((.((.........(((((((((((.((......)).)))))).))))).)).)).))))...)).))))))..((((...................)))). ( -34.51)
>consensus
CUGGGGAUCGGAUCGGUCCUGGAAUUGUAAAAUUGGGGUGUAACCCACUGUCGGCUUACACACUCAAGUCAAGCGACCAACGCCAUCCCCAU_C___________________AACCGAA
.(((((((.((...((((((.((.........(((((((((((.((......)).)))))).))))).)).)).))))....)))))))))............................. (-30.82 = -31.46 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	14,508,718 – 14,508,818
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.89
Mean single sequence MFE	-36.92
Consensus MFE	-33.54
Energy contribution	-34.14
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.91
SVM decision value	0.98
SVM RNA-class probability	0.894974
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14508718 100 - 22407834
UUCGGUU-------------------G-AUGGGGAUGGCGUUGGUCGCUUGACUUGAGUGUGUAAGCCGACAGUGGGUUACACCCCAAUUUUACAAUUCCAGGACCGAUCCGAUCCCCAG
.......-------------------.-.(((((((.(.(((((((((((.....))))((((((.(((....))).))))))...................))))))).).))))))). ( -36.50)
>DroSec_CAF1 40350 100 - 1
UUCGGUU-------------------G-AUGGGGAUGGCGUUGGUCGCUUGACUUGAGUGUGUAAGCCGACAGUGGGUUACACCCCAAUUUUACAAUUCCAGGACCGAUCCGAUCCCCAG
.......-------------------.-.(((((((.(.(((((((((((.....))))((((((.(((....))).))))))...................))))))).).))))))). ( -36.50)
>DroSim_CAF1 25053 100 - 1
UUCGGUU-------------------C-AUGGGGAUGGCGUUGGUCGCUUGACUUGAGUGUGUAAGCCGACAGUGGGUUACACCCCAAUUUUACAAUUCCAGGACCGAUCCGAUCCCCAG
.......-------------------.-.(((((((.(.(((((((((((.....))))((((((.(((....))).))))))...................))))))).).))))))). ( -36.50)
>DroEre_CAF1 33831 99 - 1
UUCAGCU-------------------G-UUGGGGAUGGCGUUGGUCGCUUGACUUGAGUGUGUAAGCCGACAGUGGGUUACACCCCAAUUUUACAAUUCCAGGACCGAUCCGAUG-CCAG
.......-------------------.-.......((((((((((((((((((....))((((((.(((....))).))))))................))))..))).))))))-))). ( -29.00)
>DroYak_CAF1 29778 120 - 1
UUCAGUUAGGUUAUGUUGGUGAGGCUGAUGGGGGAUGGCGUUGGUCGCUUGACUCGAGUGUGUAAGCCGACAGUGGGUUACACCCCAAUUUUACAAUUCCAGGACCGAUGCGAUCCCCAG
.((((((...((((....))))))))))..((((((.((((((((((((((...)))))((((((.(((....))).))))))...................))))))))).)))))).. ( -46.10)
>consensus
UUCGGUU___________________G_AUGGGGAUGGCGUUGGUCGCUUGACUUGAGUGUGUAAGCCGACAGUGGGUUACACCCCAAUUUUACAAUUCCAGGACCGAUCCGAUCCCCAG
.............................(((((((.(.(((((((((((.....))))((((((.(((....))).))))))...................))))))).).))))))). (-33.54 = -34.14 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:28 2006