Locus 584

Sequence ID	X_DroMel_CAF1
Location	1,653,337 – 1,653,453
Length	116
Max. P	0.939469

overview

Window 1

Location	1,653,337 – 1,653,453
Length	116
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	94.71
Mean single sequence MFE	-36.36
Consensus MFE	-28.98
Energy contribution	-29.46
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.22
Structure conservation index	0.80
SVM decision value	1.28
SVM RNA-class probability	0.939469
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1653337 116 + 22224390
UUUUAGCCCGCUUUCAGCGCGGUCUUAUCUUCCACGCAUAUUAUUAAUGCCUUGUCAUUAGGCGACUACUGUAUACCAUUA---UACAGGUGCAGGCGCCGACAGGAGCGGCAACAACA
.....(((.((((((.((((((.........))..((((........(((((.......)))))....(((((((....))---)))))))))..)))).))...)))))))....... ( -35.60)
>DroSec_CAF1 18181 116 + 1
UUUUAGCCCGCUUUCAGCGCGGUCUUAUCUUCCACGCAUAUUAUUAAUGCCUUGUCAUUAGGCGACUACUGUAUACCAUUA---UACAGGUGCAGGCGCCGACAGGAGCGGCAACAACA
.....(((.((((((.((((((.........))..((((........(((((.......)))))....(((((((....))---)))))))))..)))).))...)))))))....... ( -35.60)
>DroSim_CAF1 7431 116 + 1
UUUUAGCCCGCUUUCAGCGCGGUCUUAUCUUCCACGCAUAUUAUUAAUGCCUUGUCAUUAGGCGACUACUGUAUACCAUUA---UACAGGUGCAGGCGCCGACAGGAGCGGCAACAACA
.....(((.((((((.((((((.........))..((((........(((((.......)))))....(((((((....))---)))))))))..)))).))...)))))))....... ( -35.60)
>DroEre_CAF1 19803 116 + 1
GUUUGGACCGCUUUCAGCGCGGUCUUAUCUGCCACGCAUAUUAUUAAUGCCUUGUCAUUAGGCGACUACUGUAUGCCAUUA---UACAGGUGCAGGCGCCGACAGGAGCGGCAGCAACA
(((.(((((((.......)))))))...(((((.(((((.......))))((((((....((((((....)).))))....---....((((....)))))))))).).))))).))). ( -42.80)
>DroYak_CAF1 18906 115 + 1
UUUUAGCCCGUUUUCAGCGCGGUCUUAUCUGCCACGCAUAUUAUUAAUGCCUUGUCAUUAGGCGACUACUGUAUACCAUUAUAAUACAGGUGCAGGCGCCGAAAGGAG----AACAACA
.........((((((.(((((((.......)))..((((........(((((.......)))))....((((((.........))))))))))..))))(....))))----))).... ( -32.20)
>consensus
UUUUAGCCCGCUUUCAGCGCGGUCUUAUCUUCCACGCAUAUUAUUAAUGCCUUGUCAUUAGGCGACUACUGUAUACCAUUA___UACAGGUGCAGGCGCCGACAGGAGCGGCAACAACA
.......(((((....(((.((.........)).))).............((((((....((((....((((..(((...........))))))).)))))))))))))))........ (-28.98 = -29.46 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	1,653,337 – 1,653,453
Length	116
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	94.71
Mean single sequence MFE	-38.02
Consensus MFE	-28.24
Energy contribution	-29.64
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.74
SVM decision value	-0.00
SVM RNA-class probability	0.533283
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1653337 116 - 22224390
UGUUGUUGCCGCUCCUGUCGGCGCCUGCACCUGUA---UAAUGGUAUACAGUAGUCGCCUAAUGACAAGGCAUUAAUAAUAUGCGUGGAAGAUAAGACCGCGCUGAAAGCGGGCUAAAA
.......(((((....).))))((((((..(((((---((....)))))))...((((((.......))))...........((((((.........)))))).))..))))))..... ( -39.20)
>DroSec_CAF1 18181 116 - 1
UGUUGUUGCCGCUCCUGUCGGCGCCUGCACCUGUA---UAAUGGUAUACAGUAGUCGCCUAAUGACAAGGCAUUAAUAAUAUGCGUGGAAGAUAAGACCGCGCUGAAAGCGGGCUAAAA
.......(((((....).))))((((((..(((((---((....)))))))...((((((.......))))...........((((((.........)))))).))..))))))..... ( -39.20)
>DroSim_CAF1 7431 116 - 1
UGUUGUUGCCGCUCCUGUCGGCGCCUGCACCUGUA---UAAUGGUAUACAGUAGUCGCCUAAUGACAAGGCAUUAAUAAUAUGCGUGGAAGAUAAGACCGCGCUGAAAGCGGGCUAAAA
.......(((((....).))))((((((..(((((---((....)))))))...((((((.......))))...........((((((.........)))))).))..))))))..... ( -39.20)
>DroEre_CAF1 19803 116 - 1
UGUUGCUGCCGCUCCUGUCGGCGCCUGCACCUGUA---UAAUGGCAUACAGUAGUCGCCUAAUGACAAGGCAUUAAUAAUAUGCGUGGCAGAUAAGACCGCGCUGAAAGCGGUCCAAAC
.....(((((((...((((((((.((((...((((---(......))))))))).))))....))))..((((.......)))))))))))....((((((.......))))))..... ( -42.90)
>DroYak_CAF1 18906 115 - 1
UGUUGUU----CUCCUUUCGGCGCCUGCACCUGUAUUAUAAUGGUAUACAGUAGUCGCCUAAUGACAAGGCAUUAAUAAUAUGCGUGGCAGAUAAGACCGCGCUGAAAACGGGCUAAAA
....(((----(...(((((((((((((((.((((((((..((.....)).((((.((((.......)))))))))))))))).)).))))........)))))))))..))))..... ( -29.60)
>consensus
UGUUGUUGCCGCUCCUGUCGGCGCCUGCACCUGUA___UAAUGGUAUACAGUAGUCGCCUAAUGACAAGGCAUUAAUAAUAUGCGUGGAAGAUAAGACCGCGCUGAAAGCGGGCUAAAA
.......(((((....).))))((((((..(((((...........)))))...((((((.......))))...........((((((.........)))))).))..))))))..... (-28.24 = -29.64 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:33 2006