Locus 5287

Sequence ID	X_DroMel_CAF1
Location	13,851,309 – 13,851,423
Length	114
Max. P	0.600588

overview

Window 6

Location	13,851,309 – 13,851,423
Length	114
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.27
Mean single sequence MFE	-36.27
Consensus MFE	-28.55
Energy contribution	-29.83
Covariance contribution	1.28
Combinations/Pair	1.06
Mean z-score	-2.10
Structure conservation index	0.79
SVM decision value	0.14
SVM RNA-class probability	0.600588
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13851309 114 + 22224390
GUAACCUGAGUGCGGUAAGCAGCAAUCGUAACCAAUUGGCAUACCGAAUUGAAAGAUUUAUUGGACUUUUACAUGGGUCG---UCCAUGGA---CGAAUCAACAUGUGGCUGCCACCGCA
..........((((((..(((((........(((((.((....))(((((....)))))))))).....((((((..(((---((....))---))).....))))))))))).)))))) ( -38.60)
>DroSim_CAF1 4227 114 + 1
GUAACAUGAGUGCGGUAAGCAGCAAUCGUAACCAAUUGGCAUACCCAAUUGAAAGAUUUAUUGGACUUUUACAUGGGUCG---UCCGUGGA---CGAAUCAACAUGUGGCUGCCACCGCA
..........((((((..(((((((((.....(((((((.....)))))))...))))...........((((((..(((---((....))---))).....))))))))))).)))))) ( -39.20)
>DroYak_CAF1 1637 120 + 1
GUAACCUGAGUGGAGUAAGCGGGAAUAGCAACCAAUUGGCAAACCCAAUUGAAAGAUUUAUUGGACUUUUACAUGGGUCUUCUUCCAUGGACGACGAAUCAACAUGUGGCUGCCACUGCG
....((.....)).....((((...((((.(((((((((.....)))))))...((((..(((........((((((......))))))..)))..)))).....)).))))...)))). ( -31.00)
>consensus
GUAACCUGAGUGCGGUAAGCAGCAAUCGUAACCAAUUGGCAUACCCAAUUGAAAGAUUUAUUGGACUUUUACAUGGGUCG___UCCAUGGA___CGAAUCAACAUGUGGCUGCCACCGCA
..........((((((..(((((.........(((((((.....)))))))..................((((((..((((((((....)))))))).....))))))))))).)))))) (-28.55 = -29.83 +   1.28)

alignment

secondary structure

dotplot

Window 7

Location	13,851,309 – 13,851,423
Length	114
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.27
Mean single sequence MFE	-35.03
Consensus MFE	-26.54
Energy contribution	-28.60
Covariance contribution	2.06
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.76
SVM decision value	0.13
SVM RNA-class probability	0.599197
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13851309 114 - 22224390
UGCGGUGGCAGCCACAUGUUGAUUCG---UCCAUGGA---CGACCCAUGUAAAAGUCCAAUAAAUCUUUCAAUUCGGUAUGCCAAUUGGUUACGAUUGCUGCUUACCGCACUCAGGUUAC
((((((((((((.(((((.....(((---((....))---)))..)))))............((((..((((((.((....))))))))....))))))))).))))))).......... ( -36.80)
>DroSim_CAF1 4227 114 - 1
UGCGGUGGCAGCCACAUGUUGAUUCG---UCCACGGA---CGACCCAUGUAAAAGUCCAAUAAAUCUUUCAAUUGGGUAUGCCAAUUGGUUACGAUUGCUGCUUACCGCACUCAUGUUAC
((((((((((((.(((((.....(((---((....))---)))..)))))............((((..((((((((.....))))))))....))))))))).))))))).......... ( -39.80)
>DroYak_CAF1 1637 120 - 1
CGCAGUGGCAGCCACAUGUUGAUUCGUCGUCCAUGGAAGAAGACCCAUGUAAAAGUCCAAUAAAUCUUUCAAUUGGGUUUGCCAAUUGGUUGCUAUUCCCGCUUACUCCACUCAGGUUAC
.(((((((((((((((((.(((....)))..)))).....(((((((....((((..........))))....)))))))......)))))))))))...)).................. ( -28.50)
>consensus
UGCGGUGGCAGCCACAUGUUGAUUCG___UCCAUGGA___CGACCCAUGUAAAAGUCCAAUAAAUCUUUCAAUUGGGUAUGCCAAUUGGUUACGAUUGCUGCUUACCGCACUCAGGUUAC
.(((((((((((.(((((.....((((((((....))))))))..)))))..................((((((((.....))))))))........))))).))))))........... (-26.54 = -28.60 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:01 2006