Locus 2337

Sequence ID	X_DroMel_CAF1
Location	6,266,488 – 6,266,630
Length	142
Max. P	0.980417

overview

Window 5

Location	6,266,488 – 6,266,590
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.64
Mean single sequence MFE	-28.05
Consensus MFE	-20.79
Energy contribution	-20.60
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-2.22
Structure conservation index	0.74
SVM decision value	0.71
SVM RNA-class probability	0.828178
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6266488 102 + 22224390
UAAUGGGCGCCAAUGUGCAAAACACAUCACCUUUUGCCAUUCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGC------------------AAUCGCAAUGGCACGCACAAGCAAUUGAA
......(((((((((.((((((.........)))))))))).)))...((((...((((......((....))------------------....))))))))..)).(((....))).. ( -24.80)
>DroSec_CAF1 8695 102 + 1
UAAUGGGUGCCAAUGUGCAAAACACAUCACCUUUCGCCAUUCGGCAAAGCCACUAUUGCCUUCUCGCCUCUGC------------------AAUCGCAAUGGCACGCACAAGCAAUUGAA
....(((((...(((((.....))))))))))...((.....(((((........))))).....(((..(((------------------....)))..)))..)).(((....))).. ( -27.30)
>DroSim_CAF1 10053 102 + 1
UAAUGGGCGCCAAUGUGCAAAACACAUCACCUUUCGCCAUUCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGC------------------AAUCGCAAUGGCACGCACAAGCAAUUGAA
......(((...(((((.....)))))........((((((((((((........))))).....((....))------------------....).)))))).))).(((....))).. ( -23.70)
>DroYak_CAF1 5830 120 + 1
UAAUGGGCGCCAAUGUGCGAAACACAUCACCUUUCGCCAUUCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGCCAUCGCCAUCGCCAUUGCAAUAGCAAUGGCACGCACAAGCAAUUGAA
.....((((((((((.((((((.........)))))))))).)))...))).(.(((((......((....))....((....((((((((....))))))))..))....))))).).. ( -36.40)
>consensus
UAAUGGGCGCCAAUGUGCAAAACACAUCACCUUUCGCCAUUCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGC__________________AAUCGCAAUGGCACGCACAAGCAAUUGAA
...((.(((...(((((.....)))))........((((((((((((........))))).....((....))......................).)))))).))).)).......... (-20.79 = -20.60 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	6,266,488 – 6,266,590
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.64
Mean single sequence MFE	-39.90
Consensus MFE	-33.70
Energy contribution	-32.95
Covariance contribution	-0.75
Combinations/Pair	1.11
Mean z-score	-2.60
Structure conservation index	0.84
SVM decision value	1.86
SVM RNA-class probability	0.980417
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6266488 102 - 22224390
UUCAAUUGCUUGUGCGUGCCAUUGCGAUU------------------GCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGAAUGGCAAAAGGUGAUGUGUUUUGCACAUUGGCGCCCAUUA
....(((((((...(.((((.((((....------------------)))).)))).).))))))).(.(((((((((....)))))).(.(((((((.....))))))).))))).... ( -35.70)
>DroSec_CAF1 8695 102 - 1
UUCAAUUGCUUGUGCGUGCCAUUGCGAUU------------------GCAGAGGCGAGAAGGCAAUAGUGGCUUUGCCGAAUGGCGAAAGGUGAUGUGUUUUGCACAUUGGCACCCAUUA
....(((((((...(.((((.((((....------------------)))).)))).).)))))))(((((...((((.((((((((((.(.....).)))))).)))))))).))))). ( -35.20)
>DroSim_CAF1 10053 102 - 1
UUCAAUUGCUUGUGCGUGCCAUUGCGAUU------------------GCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGAAUGGCGAAAGGUGAUGUGUUUUGCACAUUGGCGCCCAUUA
....(((((((...(.((((.((((....------------------)))).)))).).))))))).(.(((((((((....)))))).(.(((((((.....))))))).))))).... ( -35.40)
>DroYak_CAF1 5830 120 - 1
UUCAAUUGCUUGUGCGUGCCAUUGCUAUUGCAAUGGCGAUGGCGAUGGCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGAAUGGCGAAAGGUGAUGUGUUUCGCACAUUGGCGCCCAUUA
....(((((((.(((.(((((((((((((((....)))))))))))))))...)))...)))))))(((((...((((.((((((((((.(.....).)))))).)))))))).))))). ( -53.30)
>consensus
UUCAAUUGCUUGUGCGUGCCAUUGCGAUU__________________GCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGAAUGGCGAAAGGUGAUGUGUUUUGCACAUUGGCGCCCAUUA
....(((((((...(.((((.((((......................)))).)))).).)))))))(((((...((((.((((((((((.(.....).)))))).)))))))).))))). (-33.70 = -32.95 +  -0.75)

alignment

secondary structure

dotplot

Window 7

Location	6,266,528 – 6,266,630
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.09
Mean single sequence MFE	-29.58
Consensus MFE	-21.23
Energy contribution	-22.97
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-3.35
Structure conservation index	0.72
SVM decision value	0.91
SVM RNA-class probability	0.879695
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6266528 102 + 22224390
UCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGC------------------AAUCGCAAUGGCACGCACAAGCAAUUGAAAUUGUAUUAAAUUGAAUUUUAAUAUAUUGCUGGAGAAACA
..(((((........)))))((((((((...((------------------....))...)))..((((((....)))....(((((((((......))))))))).)))..)))))... ( -26.90)
>DroSec_CAF1 8735 102 + 1
UCGGCAAAGCCACUAUUGCCUUCUCGCCUCUGC------------------AAUCGCAAUGGCACGCACAAGCAAUUGAAAUUGUAUUAAAUUGAAUUUUAAUAUAUUGCUGGAGAAACA
..(((((........)))))((((((((..(((------------------....)))..)))..((((((....)))....(((((((((......))))))))).)))..)))))... ( -29.30)
>DroSim_CAF1 10093 102 + 1
UCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGC------------------AAUCGCAAUGGCACGCACAAGCAAUUGAAAUUGUAUUAAAUUGAAUUUUAAUAUAUUGCCGGAGAAACA
..(((((........)))))((((((((...((------------------....))...)))..((((((....)))....(((((((((......))))))))).)))..)))))... ( -26.50)
>DroYak_CAF1 5870 120 + 1
UCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGCCAUCGCCAUCGCCAUUGCAAUAGCAAUGGCACGCACAAGCAAUUGAAAUUGUAUUAAAUUGAAUUUUAAUAUAUUGCUGGAGCAACA
..(((((........))))).....((.(((............((((((((....))))))))..((((((....)))....(((((((((......))))))))).))).))))).... ( -35.60)
>consensus
UCGGCAAAGCCACUAUUGCCUUCUCGCCUCCGC__________________AAUCGCAAUGGCACGCACAAGCAAUUGAAAUUGUAUUAAAUUGAAUUUUAAUAUAUUGCUGGAGAAACA
..(((((........)))))((((((((...((......................))...)))..((((((....)))....(((((((((......))))))))).)))..)))))... (-21.23 = -22.97 +   1.75)

alignment

secondary structure

dotplot

Window 8

Location	6,266,528 – 6,266,630
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.09
Mean single sequence MFE	-30.18
Consensus MFE	-22.14
Energy contribution	-22.20
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.84
Structure conservation index	0.73
SVM decision value	0.26
SVM RNA-class probability	0.656333
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6266528 102 - 22224390
UGUUUCUCCAGCAAUAUAUUAAAAUUCAAUUUAAUACAAUUUCAAUUGCUUGUGCGUGCCAUUGCGAUU------------------GCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGA
...(((((..(((...(((((((......)))))))((((....))))....)))..(((.((((....------------------)))).))))))))(((((........))))).. ( -24.60)
>DroSec_CAF1 8735 102 - 1
UGUUUCUCCAGCAAUAUAUUAAAAUUCAAUUUAAUACAAUUUCAAUUGCUUGUGCGUGCCAUUGCGAUU------------------GCAGAGGCGAGAAGGCAAUAGUGGCUUUGCCGA
...(((((..(((...(((((((......)))))))((((....))))....)))..(((.((((....------------------)))).))))))))(((((........))))).. ( -25.40)
>DroSim_CAF1 10093 102 - 1
UGUUUCUCCGGCAAUAUAUUAAAAUUCAAUUUAAUACAAUUUCAAUUGCUUGUGCGUGCCAUUGCGAUU------------------GCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGA
........((((((..(((((((......)))))))........(((((((...(.((((.((((....------------------)))).)))).).))))))).......)))))). ( -27.00)
>DroYak_CAF1 5870 120 - 1
UGUUGCUCCAGCAAUAUAUUAAAAUUCAAUUUAAUACAAUUUCAAUUGCUUGUGCGUGCCAUUGCUAUUGCAAUGGCGAUGGCGAUGGCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGA
(.(((((((.(((...(((((((......)))))))((((....))))....)))..((((((((((((((....))))))))))))))))).)))).).(((((........))))).. ( -43.70)
>consensus
UGUUUCUCCAGCAAUAUAUUAAAAUUCAAUUUAAUACAAUUUCAAUUGCUUGUGCGUGCCAUUGCGAUU__________________GCGGAGGCGAGAAGGCAAUAGUGGCUUUGCCGA
...(((((..(((...(((((((......)))))))((((....))))....)))..(((.((((......................)))).))))))))(((((........))))).. (-22.14 = -22.20 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:02 2006