Locus 8623

Sequence ID	X_DroMel_CAF1
Location	21,674,031 – 21,674,146
Length	115
Max. P	0.922048

overview

Window 5

Location	21,674,031 – 21,674,121
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	81.85
Mean single sequence MFE	-34.72
Consensus MFE	-26.98
Energy contribution	-30.15
Covariance contribution	3.17
Combinations/Pair	1.11
Mean z-score	-2.61
Structure conservation index	0.78
SVM decision value	1.15
SVM RNA-class probability	0.922048
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21674031 90 + 22224390
CAAGAACGGCGGCAGUUUAACAAAAAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGUCCGGUCGCUGCUGGUCGCCGAUCCCUUGG
((((..(((((((((((..........(((.....))))))))).))))).....(((((.(((((....))))).)))))....)))). ( -38.10)
>DroSec_CAF1 4433 83 + 1
CAAGAACGGCGGCAGUUUAACAAAAAAGACAACAGGUCAACUGCUC-------GCCGGCGGCCGGUCGCUGCUGGCCGCCGAUCCUUUGG
((((...((((((((((..........(((.....))))))))).)-------)))((((((((((....)))))))))).....)))). ( -38.50)
>DroSim_CAF1 5001 90 + 1
CAAGAACGGCGGCAGUUUAACAAAAAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGG
(((((.(((((((((((..........(((.....))))))))).))))).))..(((((((((((....))))))))))).....))). ( -40.70)
>DroEre_CAF1 4432 90 + 1
CAAGAACGGCGGCAGUUUAACAAAAAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGG
(((((.(((((((((((..........(((.....))))))))).))))).))..(((((((((((....))))))))))).....))). ( -40.70)
>DroYak_CAF1 5198 90 + 1
CAAGAACGGCGGCAGUUUAACAAAAAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGG
(((((.(((((((((((..........(((.....))))))))).))))).))..(((((((((((....))))))))))).....))). ( -40.70)
>DroPer_CAF1 5354 71 + 1
CAA--AAGGCAACAGUUUAACAAAAAAGGCAACCAGUCAACUGAGCGCCACUUGCAUGCACCGAAACGUUUCG-----------------
...--...((((..(.....)......(((...(((....)))...)))..))))......((((....))))----------------- (  -9.60)
>consensus
CAAGAACGGCGGCAGUUUAACAAAAAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGG
...((.(((((((((((..........(((.....))))))))).))))).))..(((((((((((....)))))))))))......... (-26.98 = -30.15 +   3.17)

alignment

secondary structure

dotplot

Window 6

Location	21,674,031 – 21,674,121
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	81.85
Mean single sequence MFE	-33.02
Consensus MFE	-22.89
Energy contribution	-25.78
Covariance contribution	2.89
Combinations/Pair	1.07
Mean z-score	-1.47
Structure conservation index	0.69
SVM decision value	0.09
SVM RNA-class probability	0.576392
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21674031 90 - 22224390
CCAAGGGAUCGGCGACCAGCAGCGACCGGACGCCGGCGAGCGGCGAGCAGUUGACCUGUUGUCUUUUUUGUUAAACUGCCGCCGUUCUUG
......(.((((((.((.(......).)).)))))))((((((((.(((((((((..(........)..))).))))))))))))))... ( -34.90)
>DroSec_CAF1 4433 83 - 1
CCAAAGGAUCGGCGGCCAGCAGCGACCGGCCGCCGGC-------GAGCAGUUGACCUGUUGUCUUUUUUGUUAAACUGCCGCCGUUCUUG
...((((((.(((((((.(......).)))))))(((-------(.(((((((((..(........)..))).)))))))))))))))). ( -35.70)
>DroSim_CAF1 5001 90 - 1
CCAAAGGAUCGGCGACCAGCAGCGACCGGCCGCCGGCGAGCGGCGAGCAGUUGACCUGUUGUCUUUUUUGUUAAACUGCCGCCGUUCUUG
......(.((((((.((.(......).)).)))))))((((((((.(((((((((..(........)..))).))))))))))))))... ( -35.30)
>DroEre_CAF1 4432 90 - 1
CCAAAGGAUCGGCGACCAGCAGCGACCGGCCGCCGGCGAGCGGCGAGCAGUUGACCUGUUGUCUUUUUUGUUAAACUGCCGCCGUUCUUG
......(.((((((.((.(......).)).)))))))((((((((.(((((((((..(........)..))).))))))))))))))... ( -35.30)
>DroYak_CAF1 5198 90 - 1
CCAAAGGAUCGGCGACCAGCAGCGACCGGCCGCCGGCGAGCGGCGAGCAGUUGACCUGUUGUCUUUUUUGUUAAACUGCCGCCGUUCUUG
......(.((((((.((.(......).)).)))))))((((((((.(((((((((..(........)..))).))))))))))))))... ( -35.30)
>DroPer_CAF1 5354 71 - 1
-----------------CGAAACGUUUCGGUGCAUGCAAGUGGCGCUCAGUUGACUGGUUGCCUUUUUUGUUAAACUGUUGCCUU--UUG
-----------------(((((.((..((((....(((((.((((..(((....)))..))))...)))))...))))..)).))--))) ( -21.60)
>consensus
CCAAAGGAUCGGCGACCAGCAGCGACCGGCCGCCGGCGAGCGGCGAGCAGUUGACCUGUUGUCUUUUUUGUUAAACUGCCGCCGUUCUUG
........((((((.((.(......).)).)))))).((((((((.(((((((((..(........)..))).))))))))))))))... (-22.89 = -25.78 +   2.89)

alignment

secondary structure

dotplot

Window 7

Location	21,674,055 – 21,674,146
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	93.74
Mean single sequence MFE	-40.16
Consensus MFE	-35.70
Energy contribution	-36.54
Covariance contribution	0.84
Combinations/Pair	1.07
Mean z-score	-1.23
Structure conservation index	0.89
SVM decision value	0.29
SVM RNA-class probability	0.672459
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21674055 91 + 22224390
AAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGUCCGGUCGCUGCUGGUCGCCGAUCCCUUGGGGCAUUGACAGUGGCAGCAGCGGCG
...........(((..(((((.((((((...(((((.(((((....))))).))))).(((....))).......))))))))))).))). ( -39.10)
>DroSec_CAF1 4457 84 + 1
AAAGACAACAGGUCAACUGCUC-------GCCGGCGGCCGGUCGCUGCUGGCCGCCGAUCCUUUGGGGCAUUGACAGUGGCAGCAGCGGCG
...........(((..(((((.-------(((((((((((((....))))))))))(.(((....)))).........)))))))).))). ( -38.40)
>DroSim_CAF1 5025 91 + 1
AAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGGGGCAUUGACAGUGGCAGCAGCGGCG
...........(((..(((((.((((((...(((((((((((....))))))))))).(((....))).......))))))))))).))). ( -41.30)
>DroEre_CAF1 4456 91 + 1
AAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGGGGCAUCGACAAUGGCAGCAGCGGUG
...(((.....))).......(((((((((((((((((((((....))))))))))(((((.....)).)))......))).).))))))) ( -40.90)
>DroYak_CAF1 5222 91 + 1
AAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGGGGCAUAGACAGUGGCAGCAGCGGUG
...(((.....)))..(((((.((((((...(((((((((((....))))))))))).(((....))).......)))))))))))..... ( -41.10)
>consensus
AAAGACAACAGGUCAACUGCUCGCCGCUCGCCGGCGGCCGGUCGCUGCUGGUCGCCGAUCCUUUGGGGCAUUGACAGUGGCAGCAGCGGCG
...(((.....)))....((.(((.(((.(((((((((((((....))))))))))(.(((....)))).........)))))).))))). (-35.70 = -36.54 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:48 2006