Locus 1432

Sequence ID	X_DroMel_CAF1
Location	4,318,373 – 4,318,467
Length	94
Max. P	0.707347

overview

Window 2

Location	4,318,373 – 4,318,467
Length	94
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	79.28
Mean single sequence MFE	-22.56
Consensus MFE	-10.56
Energy contribution	-11.56
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.47
SVM decision value	0.37
SVM RNA-class probability	0.707347
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4318373 94 + 22224390
UUUUUUUUUGCAAUGAAUU-AAGCUUAUGCUUA---CUCAAUCUAAAUAUAUGGCAAGUGAAA------UAGUGGCCACCAUGGCGUUCUGCUUGCCUUGCCAA
.........(((((((..(-((((....)))))---.)))............(((((((..((------(....(((.....))))))..)))))))))))... ( -24.10)
>DroSec_CAF1 104767 91 + 1
UUU-------CAAUGAAUUCAAGCUUAUGCUUGAAUUUCAAUCCAAAUAUAUGGCAAGUGAAA------UAGUGGCCACCAUGGCGUUCUGCUUGCCUUGCCAA
...-------...(((((((((((....))))))).))))...........(((((((..((.------(((..(((.....)))...))).))..))))))). ( -28.80)
>DroSim_CAF1 98125 88 + 1
UUU-------CAACGAAUUCAAGCUUAUGCUUA---CUCAAUCCAAAUAUAUGGCAAGUGAAA------UAGUGGCCACCAUGGCGUUCUGCUUGCCUUGCCAA
...-------..........((((....)))).---...............(((((((..((.------(((..(((.....)))...))).))..))))))). ( -20.60)
>DroEre_CAF1 111768 93 + 1
UUU-------UAAUAGGCU-AAGCUUAUACUUA---UUCAAACCAAGUAUAUGGCAUAUCAAAGCAAAGUGUUGGCCACCAUGGCGUUCUGCUUGCCUCGCCAA
...-------.....((((-((((((((((((.---........))))))...((........)).)))).))))))....(((((............))))). ( -20.30)
>DroYak_CAF1 106500 87 + 1
GUG-------AAAUAGGUG-AAACUUAUGCUUA---UUGAAAGCAAAUAUAUAGCAAAUUAAA------UGUUGGCCACCAUGGCGUUCUGCUUGCCUGGCCAA
((.-------..(((((..-...)))))((((.---....)))).........))........------..(((((((....((((.......))))))))))) ( -19.00)
>consensus
UUU_______CAAUGAAUU_AAGCUUAUGCUUA___UUCAAUCCAAAUAUAUGGCAAGUGAAA______UAGUGGCCACCAUGGCGUUCUGCUUGCCUUGCCAA
....................((((....))))...................((((................((((...))))((((.......))))..)))). (-10.56 = -11.56 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	4,318,373 – 4,318,467
Length	94
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	79.28
Mean single sequence MFE	-22.54
Consensus MFE	-13.20
Energy contribution	-12.76
Covariance contribution	-0.44
Combinations/Pair	1.33
Mean z-score	-1.79
Structure conservation index	0.59
SVM decision value	0.17
SVM RNA-class probability	0.614728
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4318373 94 - 22224390
UUGGCAAGGCAAGCAGAACGCCAUGGUGGCCACUA------UUUCACUUGCCAUAUAUUUAGAUUGAG---UAAGCAUAAGCUU-AAUUCAUUGCAAAAAAAAA
...((((((((((..(((.(((.....))).....------)))..))))))............((((---(((((....))))-.)))))))))......... ( -23.40)
>DroSec_CAF1 104767 91 - 1
UUGGCAAGGCAAGCAGAACGCCAUGGUGGCCACUA------UUUCACUUGCCAUAUAUUUGGAUUGAAAUUCAAGCAUAAGCUUGAAUUCAUUG-------AAA
.(((((((..(((.((...(((.....)))..)).------)))..)))))))....((..(..((((.(((((((....))))))))))))..-------)). ( -26.60)
>DroSim_CAF1 98125 88 - 1
UUGGCAAGGCAAGCAGAACGCCAUGGUGGCCACUA------UUUCACUUGCCAUAUAUUUGGAUUGAG---UAAGCAUAAGCUUGAAUUCGUUG-------AAA
(..((..((((((..(((.(((.....))).....------)))..))))))........(((((...---(((((....))))))))))))..-------).. ( -21.40)
>DroEre_CAF1 111768 93 - 1
UUGGCGAGGCAAGCAGAACGCCAUGGUGGCCAACACUUUGCUUUGAUAUGCCAUAUACUUGGUUUGAA---UAAGUAUAAGCUU-AGCCUAUUA-------AAA
..(((..((((..((((..((...((((.....))))..))))))...)))).((((((((.......---)))))))).....-.))).....-------... ( -24.50)
>DroYak_CAF1 106500 87 - 1
UUGGCCAGGCAAGCAGAACGCCAUGGUGGCCAACA------UUUAAUUUGCUAUAUAUUUGCUUUCAA---UAAGCAUAAGUUU-CACCUAUUU-------CAC
((((((((((.........)))....)))))))..------..................(((((....---.))))).......-.........-------... ( -16.80)
>consensus
UUGGCAAGGCAAGCAGAACGCCAUGGUGGCCACUA______UUUCACUUGCCAUAUAUUUGGAUUGAA___UAAGCAUAAGCUU_AAUUCAUUG_______AAA
.((((((((....).....(((.....)))................)))))))...................((((....)))).................... (-13.20 = -12.76 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:17 2006