Locus 34

Sequence ID	2R_DroMel_CAF1
Location	1,244,028 – 1,244,148
Length	120
Max. P	0.740985

overview

Window 0

Location	1,244,028 – 1,244,148
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-37.71
Consensus MFE	-35.24
Energy contribution	-35.05
Covariance contribution	-0.19
Combinations/Pair	1.14
Mean z-score	-1.43
Structure conservation index	0.93
SVM decision value	0.27
SVM RNA-class probability	0.661264
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1244028 120 + 20766785
UUAUUUGUCAUGACUUUUUCCCUUAUCAGCCGAGCCUCGAGUAGCUGUCCCUGGAGUAGUCGCAACGCCGCUUGAAGGGUGAAGCUACAGAGUUCACCCUCCCAGUGGCAAGCUUUGACA
.....(((((.((((..((((.....((((((.....))....)))).....)))).))))((...((((((.(.((((((((.((....)))))))))).).))))))..))..))))) ( -42.20)
>DroSim_CAF1 253 119 + 1
UUAUUUGUCAUGACUUUUUCCCUUAUCAGCCGAGCCUCGAGUAGCUGUCCCUGGAGUGGUCCCAACGCCGCUUGAAGGGUGAAGCU-CAGAGUUCACCCUCCCGGUGGCAAGCUUUGACA
.....(((((.((((..((((.....((((((.....))....)))).....)))).)))).....((((((.(.((((((((...-.....)))))))).).))))))......))))) ( -39.80)
>DroEre_CAF1 63 120 + 1
UUAUUUGUCAUGACUUUUUCCCUUAUCAGCCGAACCUCGAGUUGUUGUCCCUGGAGUAGUCCCAAAGGCGCUUGAGGGGUGAAGCUACAGUGUCCACCCUCCCAGUGGCAAGCUUUGACA
.....(((((.((((..((((.....((((((.....)).))))........)))).)))).....(.((((.(..(((((..((....))...)))))..).)))).)......))))) ( -33.42)
>DroYak_CAF1 258 120 + 1
UUAUUUGUCAUGACUUUUUCCCUUAUCAGCCGAACCUUGAAUAGCUGUCCCUGGAGUAGUCCCAAAGCCGCUUGAAGGGUGAAGCUACAGUGUUCACCCUCCCAGUGGAAAGCUUUGACA
.....(((((.((((..((((.....((((.............)))).....)))).))))......(((((.(.((((((((((....)).)))))))).).))))).......))))) ( -35.42)
>consensus
UUAUUUGUCAUGACUUUUUCCCUUAUCAGCCGAACCUCGAGUAGCUGUCCCUGGAGUAGUCCCAAAGCCGCUUGAAGGGUGAAGCUACAGAGUUCACCCUCCCAGUGGCAAGCUUUGACA
.....(((((.((((..((((.....((((((.....))....)))).....)))).)))).....((((((.(.(((((((.((......))))))))).).))))))......))))) (-35.24 = -35.05 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	1,244,028 – 1,244,148
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-39.78
Consensus MFE	-33.16
Energy contribution	-33.73
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.81
Structure conservation index	0.83
SVM decision value	0.45
SVM RNA-class probability	0.740985
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1244028 120 - 20766785
UGUCAAAGCUUGCCACUGGGAGGGUGAACUCUGUAGCUUCACCCUUCAAGCGGCGUUGCGACUACUCCAGGGACAGCUACUCGAGGCUCGGCUGAUAAGGGAAAAAGUCAUGACAAAUAA
(((((..((.((((.((.((((((((((((....)).)))))))))).)).))))..))((((..(((.....(((((...........))))).....)))...)))).)))))..... ( -44.60)
>DroSim_CAF1 253 119 - 1
UGUCAAAGCUUGCCACCGGGAGGGUGAACUCUG-AGCUUCACCCUUCAAGCGGCGUUGGGACCACUCCAGGGACAGCUACUCGAGGCUCGGCUGAUAAGGGAAAAAGUCAUGACAAAUAA
(((((..(((((((.(..((((((((((.....-...))))))))))..).)))((((((....(((.((.........)).))).))))))............))))..)))))..... ( -40.40)
>DroEre_CAF1 63 120 - 1
UGUCAAAGCUUGCCACUGGGAGGGUGGACACUGUAGCUUCACCCCUCAAGCGCCUUUGGGACUACUCCAGGGACAACAACUCGAGGUUCGGCUGAUAAGGGAAAAAGUCAUGACAAAUAA
(((((..((((.((..((((.((((((((......).)))))))))))...(((.(((((.....)))))((((..(.....)..))))))).......))...))))..)))))..... ( -35.90)
>DroYak_CAF1 258 120 - 1
UGUCAAAGCUUUCCACUGGGAGGGUGAACACUGUAGCUUCACCCUUCAAGCGGCUUUGGGACUACUCCAGGGACAGCUAUUCAAGGUUCGGCUGAUAAGGGAAAAAGUCAUGACAAAUAA
(((((..(((((((.((.(((((((((((......).)))))))))).)).))(((((((.....))))))).(((((...........))))).........)))))..)))))..... ( -38.20)
>consensus
UGUCAAAGCUUGCCACUGGGAGGGUGAACACUGUAGCUUCACCCUUCAAGCGGCGUUGGGACUACUCCAGGGACAGCUACUCGAGGCUCGGCUGAUAAGGGAAAAAGUCAUGACAAAUAA
(((((..((((.((....(((((((((((......).)))))))))).((((((((((((.....((....))......)))))))))..)))......))...))))..)))))..... (-33.16 = -33.73 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:05 2006