Locus 4209

Sequence ID	X_DroMel_CAF1
Location	11,035,932 – 11,036,040
Length	108
Max. P	0.993505

overview

Window 8

Location	11,035,932 – 11,036,040
Length	108
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	76.62
Mean single sequence MFE	-35.73
Consensus MFE	-19.69
Energy contribution	-19.88
Covariance contribution	0.19
Combinations/Pair	1.26
Mean z-score	-2.08
Structure conservation index	0.55
SVM decision value	0.59
SVM RNA-class probability	0.792867
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11035932 108 + 22224390
GGAUUCCCCAUGUUGUUUCCCUUGGGGAAAUGGACCAAUUUU--CCCCAGGCAGUUGUGGUUCGCUGAGGUUGUCCCAGAAUGGGAGAUGGAAUGUGAAUCCUU--------UUUAUU
((((((..(((.(..(((((((((((((((.........)))--))))))...(((.(((..(((....).))..))).)))))))))..).))).))))))..--------...... ( -38.10)
>DroSec_CAF1 23260 109 + 1
GAAUUACC-UCGUUGUUUCCCUUGGGGAAAUGGGCCCAUUUUUGCCCCUGGCAGUUGUGGAUCGCUGAGGUUGUCCCAAAAUGGGAGUUGGAAUGUGAAUCCUU--------UUUAUU
.....(((-((...(((((((...))))))).(..((((..(((((...)))))..))))..)...)))))..((((.....))))...(((.......)))..--------...... ( -33.80)
>DroSim_CAF1 15049 109 + 1
GGAUUCCC-UCGUUGUUUCCCUUGGGGAAAUGGGCCCAGUUUUGCCCCAGGCAGUUGUGGAUCGCUGAGGUUGUCCCAGAAUGGGAGUUGGAAUGUGAAUCCUU--------UUUAUU
((((((((-((...(((((((...))))))).(..(((...(((((...)))))...)))..)...))))...((((.....))))..........))))))..--------...... ( -35.60)
>DroYak_CAF1 18381 102 + 1
--AU-------------UCCUCCAGGGAAAUGUGGUCAUUUC-CCUACGGGCAGAUGUGGGUCACUGAGGUUGCCCCAUAAUUGGAGAUGGAAUGAGAAUCCUUUUUCCUCUUUUAUU
--..-------------..(((((((((((((....))))))-)))..((((((...(((....)))...)))))).......))))..((((.(((....))).))))......... ( -35.40)
>consensus
GGAUUCCC_UCGUUGUUUCCCUUGGGGAAAUGGGCCCAUUUU_GCCCCAGGCAGUUGUGGAUCGCUGAGGUUGUCCCAGAAUGGGAGAUGGAAUGUGAAUCCUU________UUUAUU
.................(((((((((((((((....)))))...))))))....(((.((((.((....)).)))))))...))))...(((.......)))................ (-19.69 = -19.88 +   0.19)

alignment

secondary structure

dotplot

Window 9

Location	11,035,932 – 11,036,040
Length	108
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	76.62
Mean single sequence MFE	-30.95
Consensus MFE	-15.71
Energy contribution	-16.90
Covariance contribution	1.19
Combinations/Pair	1.14
Mean z-score	-3.09
Structure conservation index	0.51
SVM decision value	2.40
SVM RNA-class probability	0.993505
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11035932 108 - 22224390
AAUAAA--------AAGGAUUCACAUUCCAUCUCCCAUUCUGGGACAACCUCAGCGAACCACAACUGCCUGGGG--AAAAUUGGUCCAUUUCCCCAAGGGAAACAACAUGGGGAAUCC
......--------..(((((...........((((.....))))...((((((((.........)).))))))--......)))))..(((((((..(....)....)))))))... ( -30.60)
>DroSec_CAF1 23260 109 - 1
AAUAAA--------AAGGAUUCACAUUCCAACUCCCAUUUUGGGACAACCUCAGCGAUCCACAACUGCCAGGGGCAAAAAUGGGCCCAUUUCCCCAAGGGAAACAACGA-GGUAAUUC
......--------..(((.......)))...((((.....))))..(((((.(.(..(((....((((...))))....)))..)).((((((...))))))....))-)))..... ( -29.20)
>DroSim_CAF1 15049 109 - 1
AAUAAA--------AAGGAUUCACAUUCCAACUCCCAUUCUGGGACAACCUCAGCGAUCCACAACUGCCUGGGGCAAAACUGGGCCCAUUUCCCCAAGGGAAACAACGA-GGGAAUCC
......--------..((((((..........((((.....))))...((((..............(((..(.......)..)))...((((((...))))))....))-)))))))) ( -33.30)
>DroYak_CAF1 18381 102 - 1
AAUAAAAGAGGAAAAAGGAUUCUCAUUCCAUCUCCAAUUAUGGGGCAACCUCAGUGACCCACAUCUGCCCGUAGG-GAAAUGACCACAUUUCCCUGGAGGA-------------AU--
.........((((..((....))..)))).(((((.......(((((......(((...)))...)))))..(((-((((((....)))))))))))))).-------------..-- ( -30.70)
>consensus
AAUAAA________AAGGAUUCACAUUCCAACUCCCAUUCUGGGACAACCUCAGCGAUCCACAACUGCCUGGGGC_AAAAUGGGCCCAUUUCCCCAAGGGAAACAACGA_GGGAAUCC
................(((.......)))...((((...(((((.....)))))...............(((((...(((((....)))))))))).))))................. (-15.71 = -16.90 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:15 2006