Locus 9703

Sequence ID	3R_DroMel_CAF1
Location	25,662,329 – 25,662,420
Length	91
Max. P	0.803915

overview

Window 9

Location	25,662,329 – 25,662,420
Length	91
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	82.11
Mean single sequence MFE	-23.73
Consensus MFE	-12.52
Energy contribution	-14.52
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.53
SVM decision value	0.63
SVM RNA-class probability	0.803915
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25662329 91 + 27905053
CUACACAAAAUUCAA-AGAAUGGGGCGAAAAAGGGGUCGAAAGGAGUAUUGUCCCCCCAUUUACAAGCGCCAGAAAGUGGCGCGCGUCACUA
...............-.((((((((.((........((....)).......)).))))))))....((((((.....))))))......... ( -27.26)
>DroSec_CAF1 8775 88 + 1
CUGCACAAAAUUAAA-AGAAUGGGGCAAAAAAGACAUCGAAC---AUAUUGUCCCCCCACUUACAAGCGCCAGAAAGUGGCGCGCAUCACCA
.(((...........-....(((((.......((((......---....)))).))))).......((((((.....)))))))))...... ( -22.50)
>DroSim_CAF1 9706 88 + 1
CUGCACAAAAUUAAA-AGAAUGGGGCAAAAGAGACAUCGAAC---AUAUUGUCCCCCCACUUACAAGCGCCAGAAAGUGGCGCGCAUCACCA
.(((...........-....(((((.....(.((((......---....)))))))))).......((((((.....)))))))))...... ( -23.30)
>DroEre_CAF1 8839 91 + 1
UAACACAAAAUCCGA-GGAAUGGAGAGAAGAAAGCGUGGACAUAUGUAUUGUCCACCCAUUUACAAGAGCCAGAAAGUGGCGCGCAUCACCA
..........((...-.)).(((.((...(...(((((((((.......)))))))............((((.....)))))).).)).))) ( -21.40)
>DroYak_CAF1 9633 92 + 1
UUACACAAAAUCCAAAAGAAUGGAGGGAAAAAAGCGUGGACAUGUGUAUUGUCCACCCAUUUACAAGAGCCAGAAAGUGGCGCGCAUCACCA
..........((((......))))((((.....(((((((((.......)))))))............((((.....))))))...)).)). ( -24.20)
>consensus
CUACACAAAAUUCAA_AGAAUGGGGCGAAAAAGGCGUCGAAA___GUAUUGUCCCCCCAUUUACAAGCGCCAGAAAGUGGCGCGCAUCACCA
.................((((((((.((.......................)).))))))))....((((((.....))))))......... (-12.52 = -14.52 +   2.00)

alignment

secondary structure

dotplot

Window 0

Location	25,662,329 – 25,662,420
Length	91
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	82.11
Mean single sequence MFE	-25.08
Consensus MFE	-17.36
Energy contribution	-16.80
Covariance contribution	-0.56
Combinations/Pair	1.24
Mean z-score	-1.56
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.518943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25662329 91 - 27905053
UAGUGACGCGCGCCACUUUCUGGCGCUUGUAAAUGGGGGGACAAUACUCCUUUCGACCCCUUUUUCGCCCCAUUCU-UUGAAUUUUGUGUAG
.....((((((((((.....)))))).....((((((((((......)))...(((........))))))))))..-.........)))).. ( -26.90)
>DroSec_CAF1 8775 88 - 1
UGGUGAUGCGCGCCACUUUCUGGCGCUUGUAAGUGGGGGGACAAUAU---GUUCGAUGUCUUUUUUGCCCCAUUCU-UUUAAUUUUGUGCAG
......(((((((((.....)))))).....(((((((((((.....---))))(....).......)))))))..-...........))). ( -25.60)
>DroSim_CAF1 9706 88 - 1
UGGUGAUGCGCGCCACUUUCUGGCGCUUGUAAGUGGGGGGACAAUAU---GUUCGAUGUCUCUUUUGCCCCAUUCU-UUUAAUUUUGUGCAG
......(((((((((.....)))))).....(((((((((((.....---))))((....)).....)))))))..-...........))). ( -26.20)
>DroEre_CAF1 8839 91 - 1
UGGUGAUGCGCGCCACUUUCUGGCUCUUGUAAAUGGGUGGACAAUACAUAUGUCCACGCUUUCUUCUCUCCAUUCC-UCGGAUUUUGUGUUA
...((((((((((((.....))))............(((((((.......))))))))).........(((.....-..)))....)))))) ( -21.80)
>DroYak_CAF1 9633 92 - 1
UGGUGAUGCGCGCCACUUUCUGGCUCUUGUAAAUGGGUGGACAAUACACAUGUCCACGCUUUUUUCCCUCCAUUCUUUUGGAUUUUGUGUAA
......(((((((((.....))))..........(.(((((((.......))))))).).........((((......))))....))))). ( -24.90)
>consensus
UGGUGAUGCGCGCCACUUUCUGGCGCUUGUAAAUGGGGGGACAAUAC___UUUCGACGCCUUUUUCGCCCCAUUCU_UUGAAUUUUGUGUAG
.......((((((((.....)))).......(((((((.((.......................)).)))))))............)))).. (-17.36 = -16.80 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:13 2006