Locus 821

Sequence ID	2R_DroMel_CAF1
Location	3,870,389 – 3,870,516
Length	127
Max. P	0.804752

overview

Window 4

Location	3,870,389 – 3,870,498
Length	109
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	87.63
Mean single sequence MFE	-25.96
Consensus MFE	-22.59
Energy contribution	-22.65
Covariance contribution	0.06
Combinations/Pair	1.09
Mean z-score	-1.64
Structure conservation index	0.87
SVM decision value	0.57
SVM RNA-class probability	0.784096
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3870389 109 + 20766785
AAAUUCCACUUUCAUUAAA---AGUUUCGGCUAAUGUUUUGGUCCUCCCUACUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCGAAUAAACCCCCAAAACCUCCAAGUC------
.......(((((.....))---)))...((((...(((((((............(((((((...((((......)))))))))))...........))))))).....))))------ ( -23.50)
>DroSec_CAF1 126146 109 + 1
AAAUUCCAUUUUCAUUAAA---AGUUUUGGCUAAUGUUUUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCGAAUAAGCCCCCAAAGCCUCCAAGUC------
...................---...(((((.....(((((((.........(..(((((((...((((......)))))))))))..)........)))))))..)))))..------ ( -24.83)
>DroEre_CAF1 127156 118 + 1
AAAUUCCGUUUUCAUUCAAAGAAGUUUUGGCUAAUGUUUUGGUCCUCCCUUUUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCAAGUAAGCCCCCCAAGCCUCCAAAUCCUCCAC
...................(((((....((((((....))))))....)))))..(((((((..((((......))))((((.........))))....))))).))........... ( -25.90)
>DroYak_CAF1 124518 112 + 1
AAAUUCCAUUUUCAUUAAAACAAGUUUUGGCCAAUGUUUUGGUCCUCUUUAUUAAGGGGCUUCAGCUCACGUAAGAGCGGCUCCUCAAGCAAGCCCCCAAAGCCUCCAAAUC------
.......................(((((((((((....)))))............(((((((..((((......)))).(((.....)))))))))))))))).........------ ( -29.60)
>consensus
AAAUUCCAUUUUCAUUAAA___AGUUUUGGCUAAUGUUUUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCAAAUAAGCCCCCAAAGCCUCCAAAUC______
.........................(((((.....(((((((............(((((((...((((......)))))))))))...........)))))))..)))))........ (-22.59 = -22.65 +   0.06)

alignment

secondary structure

dotplot

Window 5

Location	3,870,424 – 3,870,516
Length	92
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	87.22
Mean single sequence MFE	-24.52
Consensus MFE	-23.02
Energy contribution	-23.40
Covariance contribution	0.38
Combinations/Pair	1.05
Mean z-score	-1.52
Structure conservation index	0.94
SVM decision value	0.63
SVM RNA-class probability	0.804752
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3870424 92 + 20766785
UUGGUCCUCCCUACUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCGAAUAAACCCCCAAAACCUCCAAGUC---------CACCGAAGCCACCAUCGU
.((((....(((....)))((((((.((((......))))((((..........................))))---------....)))))))))).... ( -22.07)
>DroSec_CAF1 126181 92 + 1
UUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCGAAUAAGCCCCCAAAGCCUCCAAGUC---------CACCGAAGCCGCCAUCGU
.((((....(((....)))((((((.((((......))))((((.........)))).................---------....)))))))))).... ( -26.20)
>DroEre_CAF1 127194 101 + 1
UUGGUCCUCCCUUUUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCAAGUAAGCCCCCCAAGCCUCCAAAUCCUCCACAUCCGCCGAAGCCGCCAUCGU
.((((....(((....)))((((((.((((......))))((((.........))))..............................)))))))))).... ( -26.00)
>DroYak_CAF1 124556 92 + 1
UUGGUCCUCUUUAUUAAGGGGCUUCAGCUCACGUAAGAGCGGCUCCUCAAGCAAGCCCCCAAAGCCUCCAAAUC---------CACCGAAGCCUCCAUCGU
.................((((((((.((((......))))((((.........)))).................---------....)))))).))..... ( -23.80)
>consensus
UUGGUCCUCCCUAUUAAGGGGCUUCAGCUCACGUCAGAGCGGCUCCUCAAAUAAGCCCCCAAAGCCUCCAAAUC_________CACCGAAGCCGCCAUCGU
.(((((((........)))((((((.((((......))))((((.........))))..............................)))))))))).... (-23.02 = -23.40 +   0.38)

alignment

secondary structure

dotplot

Window 6

Location	3,870,424 – 3,870,516
Length	92
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-34.65
Consensus MFE	-30.51
Energy contribution	-30.07
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-1.49
Structure conservation index	0.88
SVM decision value	0.30
SVM RNA-class probability	0.679601
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3870424 92 - 20766785
ACGAUGGUGGCUUCGGUG---------GACUUGGAGGUUUUGGGGGUUUAUUCGAGGAGCCGCUCUGACGUGAGCUGAAGCCCCUUAGUAGGGAGGACCAA
....(((((((((((((.---------.(((..((((((((..(((....)))..))))))..))..).))..)))))))))((((......)))))))). ( -32.60)
>DroSec_CAF1 126181 92 - 1
ACGAUGGCGGCUUCGGUG---------GACUUGGAGGCUUUGGGGGCUUAUUCGAGGAGCCGCUCUGACGUGAGCUGAAGCCCCUUAAUAGGGAGGACCAA
....(((.(((((((((.---------..((((((((((.....))))..))))))..)))((((......)))).))))))((((......)))).))). ( -35.30)
>DroEre_CAF1 127194 101 - 1
ACGAUGGCGGCUUCGGCGGAUGUGGAGGAUUUGGAGGCUUGGGGGGCUUACUUGAGGAGCCGCUCUGACGUGAGCUGAAGCCCCUUAAAAGGGAGGACCAA
....(((.(((((((((..((((((((....(((...((..((.......))..))...))))))).))))..)))))))))((((......)))).))). ( -37.40)
>DroYak_CAF1 124556 92 - 1
ACGAUGGAGGCUUCGGUG---------GAUUUGGAGGCUUUGGGGGCUUGCUUGAGGAGCCGCUCUUACGUGAGCUGAAGCCCCUUAAUAAAGAGGACCAA
....(((.(((((((...---------........((((((..(((....)))..))))))((((......)))))))))))((((......)))).))). ( -33.30)
>consensus
ACGAUGGCGGCUUCGGUG_________GACUUGGAGGCUUUGGGGGCUUACUCGAGGAGCCGCUCUGACGUGAGCUGAAGCCCCUUAAUAGGGAGGACCAA
....(((.(((((((....................((((((..(((....)))..))))))((((......)))))))))))((((......)))).))). (-30.51 = -30.07 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:15 2006