Locus 4570

Sequence ID	X_DroMel_CAF1
Location	11,994,828 – 11,994,940
Length	112
Max. P	0.995419

overview

Window 3

Location	11,994,828 – 11,994,940
Length	112
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	87.78
Mean single sequence MFE	-43.81
Consensus MFE	-31.01
Energy contribution	-33.33
Covariance contribution	2.31
Combinations/Pair	1.09
Mean z-score	-2.85
Structure conservation index	0.71
SVM decision value	1.19
SVM RNA-class probability	0.928551
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11994828 112 + 22224390
GUGUGUGUUUAGGAGGAGGAGCGGAUGCAGGGGCAUGUGAUGGCACUUGCCCUUUGACCCCUGCCCCUUUUGCCCCUCAUUGUUUGGGGCACAACAAAAAGCAAAUAAAGAU
.(((.(((((...((((((.((((..(((((((((.(((....))).))))).))).)..)))).))))))(((((.........)))))........))))).)))..... ( -39.30)
>DroSec_CAF1 33845 112 + 1
GUGUGUGUUUAGGAGGGGGAGGGGCUUCAGGGGCAUGUGAUGGCACUUGCCCUUCGACCCCUGCCCCUUUGGCCCCUCAUUGUUUGGGGUACAACAAAAAGCAAAUAAAGAC
.(((.(((((.(((((((.(((((.((.(((((((.(((....))).))))))).))))))).))))))).(((((.........)))))........))))).)))..... ( -50.80)
>DroEre_CAF1 32714 107 + 1
G----GGGAUGGGGG-GGGGGAGGGUGCAAGGGCACGUGAUGGCACUUGCCCUUUGACCCCUGCCCCAUUGGCCCCUCAUUGUUUGGAGUACAACAAAAAGCAAAUAAAGAU
(----(((.....((-((.((.((((..(((((((.(((....))).)))))))..)))))).)))).....))))((.(((((((...............))))))).)). ( -46.56)
>DroYak_CAF1 33875 111 + 1
GUGUGUGUUUAGGAG-AGGGGAGGGUGCAAGGGCAUGUGAUGGCACUUGCCCUUUGACCCCUGCCCCAUUUGCCCCUCAUUGUUUGGGAUACAACAAAAAGCAAAUAAAGAU
.(((((.....(.((-(((((((((..((((((((.(((....))).))))).)))..)))).)))).))).)(((.........))))))))................... ( -38.60)
>consensus
GUGUGUGUUUAGGAG_AGGAGAGGGUGCAAGGGCAUGUGAUGGCACUUGCCCUUUGACCCCUGCCCCAUUGGCCCCUCAUUGUUUGGGGUACAACAAAAAGCAAAUAAAGAU
......((((.(((((((.((.((((..(((((((.(((....))).)))))))..)))))).))))))).(((((.........)))))........)))).......... (-31.01 = -33.33 +   2.31)

alignment

secondary structure

dotplot

Window 4

Location	11,994,828 – 11,994,940
Length	112
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	87.78
Mean single sequence MFE	-42.40
Consensus MFE	-36.34
Energy contribution	-37.40
Covariance contribution	1.06
Combinations/Pair	1.06
Mean z-score	-4.26
Structure conservation index	0.86
SVM decision value	2.57
SVM RNA-class probability	0.995419
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11994828 112 - 22224390
AUCUUUAUUUGCUUUUUGUUGUGCCCCAAACAAUGAGGGGCAAAAGGGGCAGGGGUCAAAGGGCAAGUGCCAUCACAUGCCCCUGCAUCCGCUCCUCCUCCUAAACACACAC
.......(((((((((..((((.......))))..)))))))))(((((.((((((....(((((.(((....))).)))))........)))))).))))).......... ( -39.50)
>DroSec_CAF1 33845 112 - 1
GUCUUUAUUUGCUUUUUGUUGUACCCCAAACAAUGAGGGGCCAAAGGGGCAGGGGUCGAAGGGCAAGUGCCAUCACAUGCCCCUGAAGCCCCUCCCCCUCCUAAACACACAC
((.((((...((((((..((((.......))))..))))))...(((((.((((((....(((((.(((....))).))))).....)))))).)))))..)))).)).... ( -43.00)
>DroEre_CAF1 32714 107 - 1
AUCUUUAUUUGCUUUUUGUUGUACUCCAAACAAUGAGGGGCCAAUGGGGCAGGGGUCAAAGGGCAAGUGCCAUCACGUGCCCUUGCACCCUCCCCC-CCCCCAUCCC----C
..........((((((..((((.......))))..))))))..((((((..((((...(((((((.(((....))).))))))).......)))).-.))))))...----. ( -41.90)
>DroYak_CAF1 33875 111 - 1
AUCUUUAUUUGCUUUUUGUUGUAUCCCAAACAAUGAGGGGCAAAUGGGGCAGGGGUCAAAGGGCAAGUGCCAUCACAUGCCCUUGCACCCUCCCCU-CUCCUAAACACACAC
......((((((((((..((((.......))))..))))))))))((((.((((....(((((((.(((....))).)))))))...)))))))).-............... ( -45.20)
>consensus
AUCUUUAUUUGCUUUUUGUUGUACCCCAAACAAUGAGGGGCAAAAGGGGCAGGGGUCAAAGGGCAAGUGCCAUCACAUGCCCCUGCACCCUCCCCC_CUCCUAAACACACAC
.......(((((((((..((((.......))))..))))))))).((((.(((((...(((((((.(((....))).))))))).......))))).))))........... (-36.34 = -37.40 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:24 2006