Locus 1594

Sequence ID	2R_DroMel_CAF1
Location	5,963,951 – 5,964,052
Length	101
Max. P	0.859204

overview

Window 5

Location	5,963,951 – 5,964,052
Length	101
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	78.50
Mean single sequence MFE	-33.03
Consensus MFE	-24.84
Energy contribution	-25.28
Covariance contribution	0.45
Combinations/Pair	1.09
Mean z-score	-1.35
Structure conservation index	0.75
SVM decision value	0.65
SVM RNA-class probability	0.812605
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5963951 101 + 20766785
GCGGUCUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGUCUGAAGGCCUCCCACUUGGGGCCAUGCCUGAAUGAGGUACAA---AAAAAAAUAAUGUGCAA-AAA
(((((....((((.((((((((.(((...))).))))).)))..)))).(((....)))))).(((((.....)))))...---.............))..-... ( -32.90)
>DroPse_CAF1 3102 82 + 1
GCCGUUUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGCCUGAAGGCCUCCCACUUGGGUCCGUGCCUGCG----------------------GUGGGCAA-GAG
((((....))))(((((((.....))))))).(((.((((((.(((((.(((....)))...).))))...----------------------.)))))).-))) ( -37.70)
>DroSim_CAF1 6632 102 + 1
GCGGUCUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGUCUGAAGGCCUCCCACUUGGGACCAUGCCUGAAUAAGGUACAACAAAAAAAAA--AUGUGCAA-AAA
((((((...((((.((((((((.(((...))).))))).)))..))))..((....)))))).(((((.....))))).............--....))..-... ( -33.80)
>DroEre_CAF1 6675 82 + 1
GCGGUCUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGUCUGAAGGCCUCCCACUUGGGACCGUGCCUGAAUAAAGUAG-----------------------AAU
....(((((((((.((((((((.(((...))).))))).)))..))))((((....))))...............))))-----------------------).. ( -30.10)
>DroYak_CAF1 6844 95 + 1
GCGGUCUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGUCUGAAGGCCUCCCACUUGGGACCAUGCCUGAAUGAAGUAA--------AAAA--AAGUGCAAAAAA
..((((...((((.((((((((.(((...))).))))).)))..))))..((....)))))).(((((...........--------....--.)).)))..... ( -28.69)
>DroPer_CAF1 3107 82 + 1
GCCGUUUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGUCUGAAGGCCUCCCACUUGGGUCCGUGCCUGCG----------------------GUGGGCAA-GAG
((((....))))(((((((.....))))))).(((.((((((.(((((.(((....)))...).))))...----------------------.)))))).-))) ( -35.00)
>consensus
GCGGUCUGCGGCUGCAGCAGGAUGUGCUGCACCUCCUGUCUGAAGGCCUCCCACUUGGGACCAUGCCUGAAU_A_GUA_______________AUGUGCAA_AAA
(((((.....))))).((((((.(((...))).))))))....((((.((((....))))....))))..................................... (-24.84 = -25.28 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	5,963,951 – 5,964,052
Length	101
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	78.50
Mean single sequence MFE	-32.02
Consensus MFE	-26.27
Energy contribution	-26.27
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.82
SVM decision value	0.82
SVM RNA-class probability	0.859204
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5963951 101 - 20766785
UUU-UUGCACAUUAUUUUUUU---UUGUACCUCAUUCAGGCAUGGCCCCAAGUGGGAGGCCUUCAGACAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAGACCGC
..(-((((...........((---((((.(((.....)))...((((((.....)).)))).....))))))(((((((((.....))))))).))))))).... ( -32.20)
>DroPse_CAF1 3102 82 - 1
CUC-UUGCCCAC----------------------CGCAGGCACGGACCCAAGUGGGAGGCCUUCAGGCAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAAACGGC
(((-(((((...----------------------.(.((((.(...(((....))).))))).).)))))))).(((((((.....)))))))((((....)))) ( -37.50)
>DroSim_CAF1 6632 102 - 1
UUU-UUGCACAU--UUUUUUUUUGUUGUACCUUAUUCAGGCAUGGUCCCAAGUGGGAGGCCUUCAGACAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAGACCGC
...-..((....--........(((((((((((..((((((....((((....)))).))))...))...))))))))))).......((((....))))...)) ( -32.70)
>DroEre_CAF1 6675 82 - 1
AUU-----------------------CUACUUUAUUCAGGCACGGUCCCAAGUGGGAGGCCUUCAGACAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAGACCGC
...-----------------------................(((((....((((...((((((.....))))))((((((.....))))))..)))).))))). ( -28.60)
>DroYak_CAF1 6844 95 - 1
UUUUUUGCACUU--UUUU--------UUACUUCAUUCAGGCAUGGUCCCAAGUGGGAGGCCUUCAGACAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAGACCGC
...(((((....--....--------..(((((..((((((....((((....)))).))))...))...)))))((((((.....))))))....))))).... ( -30.00)
>DroPer_CAF1 3107 82 - 1
CUC-UUGCCCAC----------------------CGCAGGCACGGACCCAAGUGGGAGGCCUUCAGACAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAAACGGC
.((-(((((...----------------------....)))).)))(((....)))..((((((.....))))))((((((.....)))))).((((....)))) ( -31.10)
>consensus
UUU_UUGCACAU_______________UAC_U_AUUCAGGCACGGUCCCAAGUGGGAGGCCUUCAGACAGGAGGUGCAGCACAUCCUGCUGCAGCCGCAGACCGC
......................................(((.....(((....)))..((((((.....))))))((((((.....)))))).)))......... (-26.27 = -26.27 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:27 2006