Locus 4587

Sequence ID	X_DroMel_CAF1
Location	12,023,773 – 12,023,868
Length	95
Max. P	0.958888

overview

Window 7

Location	12,023,773 – 12,023,868
Length	95
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	83.22
Mean single sequence MFE	-31.25
Consensus MFE	-21.98
Energy contribution	-22.29
Covariance contribution	0.31
Combinations/Pair	1.17
Mean z-score	-2.09
Structure conservation index	0.70
SVM decision value	0.93
SVM RNA-class probability	0.884748
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12023773 95 + 22224390
UUUAGUUGCCAUUAAAUGGCAUC----------CCACCCAAAAAACUACGCCCCUGACUCACUUACAUGGGUGUUGUUAUUUCCAGGGGCUGUU---UUUCAACGGGG
......((((((...)))))).(----------((.....((((((...(((((((((.(((((....)))))..))......))))))).)))---))).....))) ( -29.90)
>DroSec_CAF1 56120 94 + 1
UUUAGUUGCCAUUAAAGGGCGCC----------CCUCCCGA-AAACUACGCCCCUGCCUCACUUACAUGGGUGUUGUUAUUUCCAGGGGCUGUU---UUUCCAGGGGG
.......(((.......))).((----------(((...((-((((...((((((((..(((((....)))))..).......))))))).)))---)))..))))). ( -32.41)
>DroSim_CAF1 54723 94 + 1
UUUAGUUGCCAUUAAAGGGCGCC----------CCUCCCGA-AAACUACGCCCCUGCCUCACUUACAUGGGUGUUGUUAUUUCCAGGGGCUGUU---UUUACAAGGGG
.......(((.......))).((----------(((...((-((((...((((((((..(((((....)))))..).......))))))).)))---)))...))))) ( -31.41)
>DroYak_CAF1 53940 107 + 1
UUUAGUCGCCAUUAAGAGGUGCCUCCCCACCCCCCCCCCGCGAAACUACGCCCCUGACUCACUUACAUGGGUGUUGUUAUUUCCAGGGGCUGUUAUUUCCAUAGG-GG
...((.((((.......)))).))...........((((..((((..(((((((((((.(((((....)))))..))......))))))).))..))))....))-)) ( -31.30)
>consensus
UUUAGUUGCCAUUAAAGGGCGCC__________CCUCCCGA_AAACUACGCCCCUGACUCACUUACAUGGGUGUUGUUAUUUCCAGGGGCUGUU___UUUACAGGGGG
......((((.......)))).............(((((........(((((((((...(((((....)))))..........))))))).))..........))))) (-21.98 = -22.29 +   0.31)

alignment

secondary structure

dotplot

Window 8

Location	12,023,773 – 12,023,868
Length	95
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	83.22
Mean single sequence MFE	-35.50
Consensus MFE	-21.59
Energy contribution	-22.65
Covariance contribution	1.06
Combinations/Pair	1.15
Mean z-score	-2.96
Structure conservation index	0.61
SVM decision value	1.49
SVM RNA-class probability	0.958888
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12023773 95 - 22224390
CCCCGUUGAAA---AACAGCCCCUGGAAAUAACAACACCCAUGUAAGUGAGUCAGGGGCGUAGUUUUUUGGGUGG----------GAUGCCAUUUAAUGGCAACUAAA
(((..(..(((---(((.((((((((.....((.(((....)))..))...))))))))...))))))..)..))----------).((((((...))))))...... ( -33.50)
>DroSec_CAF1 56120 94 - 1
CCCCCUGGAAA---AACAGCCCCUGGAAAUAACAACACCCAUGUAAGUGAGGCAGGGGCGUAGUUU-UCGGGAGG----------GGCGCCCUUUAAUGGCAACUAAA
(((((((((((---....((((((((......)....(((((....))).)))))))))....)))-))))).))----------)..(((.......)))....... ( -35.80)
>DroSim_CAF1 54723 94 - 1
CCCCUUGUAAA---AACAGCCCCUGGAAAUAACAACACCCAUGUAAGUGAGGCAGGGGCGUAGUUU-UCGGGAGG----------GGCGCCCUUUAAUGGCAACUAAA
((((((.(.((---(((.((((((((......)....(((((....))).)))))))))...))))-).).))))----------)).(((.......)))....... ( -33.50)
>DroYak_CAF1 53940 107 - 1
CC-CCUAUGGAAAUAACAGCCCCUGGAAAUAACAACACCCAUGUAAGUGAGUCAGGGGCGUAGUUUCGCGGGGGGGGGGUGGGGAGGCACCUCUUAAUGGCGACUAAA
((-((..(((((.((...((((((((.....((.(((....)))..))...)))))))).)).)))))..))))(((((((......))))))).............. ( -39.20)
>consensus
CCCCCUGGAAA___AACAGCCCCUGGAAAUAACAACACCCAUGUAAGUGAGGCAGGGGCGUAGUUU_UCGGGAGG__________GGCGCCCUUUAAUGGCAACUAAA
((.((((((((....((.((((((((......)..(((........)))...)))))))))...)))))))).)).............(((.......)))....... (-21.59 = -22.65 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:53 2006