Locus 7601

Sequence ID	X_DroMel_CAF1
Location	18,952,547 – 18,952,690
Length	143
Max. P	0.998558

overview

Window 2

Location	18,952,547 – 18,952,655
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.33
Mean single sequence MFE	-28.62
Consensus MFE	-25.78
Energy contribution	-25.86
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.90
SVM decision value	3.14
SVM RNA-class probability	0.998558
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18952547 108 + 22224390
--------CGCCCGCA-AACGCAUAAACAACAAUUUCACAGGGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA-
--------.....((.-...))................(((((((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).))))))))....- ( -30.90)
>DroSec_CAF1 20711 108 + 1
--------CGCCCGCA-AACGCAUAAACAACAAUUUCACAGGGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA-
--------.....((.-...))................(((((((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).))))))))....- ( -30.90)
>DroSim_CAF1 9223 108 + 1
--------CGCCCGCA-AACGCAUAAACAACAAUUUCACAGGGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA-
--------.....((.-...))................(((((((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).))))))))....- ( -30.90)
>DroEre_CAF1 21437 108 + 1
--------CGCCCGCA-AACGCAUAAACAACAAUUUCACAGCGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA-
--------.....((.-...))................(((.(((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).)))).)))....- ( -23.80)
>DroYak_CAF1 11116 120 + 1
GCCGCAAACGCCCGCAAAACGCAUAAACAACAAUUUCACAGGACCUGGCAGGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGACCUGCCCAC
.((((....))..((.....))..................))....((((((.((((.((...((....((..((((((.........))))))..))....)))).))))))))))... ( -26.60)
>consensus
________CGCCCGCA_AACGCAUAAACAACAAUUUCACAGGGCCUG__AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA_
.............(((....((((..............((((((((....))))))))(((...)))))))..((((((.........))))))..((((.......))))..))).... (-25.78 = -25.86 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	18,952,578 – 18,952,690
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.62
Mean single sequence MFE	-34.80
Consensus MFE	-28.48
Energy contribution	-28.92
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.82
SVM decision value	0.52
SVM RNA-class probability	0.768933
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18952578 112 + 22224390
GGGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA----CCACGGGC--UCAAAGUCGACCGGAAAAGCUGGGAAA
(((((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).)))))).((((.----....))))--..........((((.....)))).... ( -37.10)
>DroSec_CAF1 20742 112 + 1
GGGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA----CAACGGGC--UCAAAGUCGACCGGAAGAGCUGGGAAA
(((((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).)))))).((((.----....))))--..........((((.....)))).... ( -37.10)
>DroSim_CAF1 9254 112 + 1
GGGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA----CAACGGGC--UCAAAGUCGACCGGAAGAGCUGGGAAA
(((((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).)))))).((((.----....))))--..........((((.....)))).... ( -37.10)
>DroEre_CAF1 21468 112 + 1
GCGCCUG--AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA----CAACGGGC--UCAAAGUCGACCGGAAAAGCUGGGAAA
..(((((--(((((...((.....(.....)..((((((.........))))))...)).)))))).))))...((((.----....))))--..........((((.....)))).... ( -30.40)
>DroYak_CAF1 11156 120 + 1
GGACCUGGCAGGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGACCUGCCCACACACAACAGGCUCUCAAAGUCGACCGGAAAAGCUGGGAAA
...((..((....((((((..........((..((((((.........))))))..))....(((..((..((((...........))))..))..)))....))))))..))..))... ( -32.30)
>consensus
GGGCCUG__AAGGUUCUGGAUAAAGUCAUGCACUUGGCUCGUAAAUAAAGCCAAAAGCCUAUCUUCAAGGCCCUGCCCA____CAACGGGC__UCAAAGUCGACCGGAAAAGCUGGGAAA
((((((...(((((...((.....(.....)..((((((.........))))))...)).)))))..)))))).((((.........))))............((((.....)))).... (-28.48 = -28.92 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:01 2006