Locus 140

Sequence ID	2L_DroMel_CAF1
Location	429,409 – 429,519
Length	110
Max. P	0.999997

overview

Window 8

Location	429,409 – 429,519
Length	110
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	94.78
Mean single sequence MFE	-37.84
Consensus MFE	-38.64
Energy contribution	-38.80
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-3.47
Structure conservation index	1.02
SVM decision value	6.14
SVM RNA-class probability	0.999997
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 429409 110 + 22407834
AAAAGGCCAGAAAUGCGCGCCAAUUCCGCAAAAGCGAUUCUCUGGACCGGGAGACUGGAGACUGAAAUCGACUUCAAGGAAUUGCAUAAAACAUUUUUGGCCGUUCUUUU--------
....(((((((((((.(((.......)))....(((((((..((((((((....)))).((......))...))))..)))))))......)))))))))))........-------- ( -40.60)
>DroSec_CAF1 6920 110 + 1
AAAAGGCCAGAAAUGCGCGCCAAUUCCGCAAAAGCGAUUCUCUGGACCGGGAGACUGGAGACUGAAAUCGACUUCAAGGAAUUGCAUAAAACAUUUUUGGCCGUUCUUUU--------
....(((((((((((.(((.......)))....(((((((..((((((((....)))).((......))...))))..)))))))......)))))))))))........-------- ( -40.60)
>DroSim_CAF1 5907 110 + 1
AAAAGGCCAGAAAUGCGCGCCAAUUCCGCAAAAGCGAUUCUCUGGACCGGGAGACUGGAGACUGAAAUCGACUUCAAGGAAUUGCAUAAAACAUUUUUGGCCGUUCUUUU--------
....(((((((((((.(((.......)))....(((((((..((((((((....)))).((......))...))))..)))))))......)))))))))))........-------- ( -40.60)
>DroEre_CAF1 6654 114 + 1
-AAAGGCCAGA-AUGCGCGCCAAUUCCGCAAAAGCGAUUCUCUGGACCGGGAGACUGGAGACUGAAAUCGACUUCAAGGAAUUGCAUAAAACAUUUUUGGUCGUUCUUUUUUAUUU--
-...(((((((-(((((.(......)))))...(((((((..((((((((....)))).((......))...))))..))))))).........))))))))..............-- ( -33.70)
>DroYak_CAF1 6278 117 + 1
AAAAGGCCAGA-AUGCGCGCCAAUUCCGCAAAAGCGAUUCUCUGGACCGGGAGACUGGAGACUGAAAUCGACUUCAAGGAAUUGCAUAAAACAUUUUUGGUCGUUCUUUUUUAUUUUU
....(((((((-(((((.(......)))))...(((((((..((((((((....)))).((......))...))))..))))))).........))))))))................ ( -33.70)
>consensus
AAAAGGCCAGAAAUGCGCGCCAAUUCCGCAAAAGCGAUUCUCUGGACCGGGAGACUGGAGACUGAAAUCGACUUCAAGGAAUUGCAUAAAACAUUUUUGGCCGUUCUUUU________
....(((((((((((.(((.......)))....(((((((..((((((((....)))).((......))...))))..)))))))......)))))))))))................ (-38.64 = -38.80 +   0.16)

alignment

secondary structure

dotplot

Window 9

Location	429,409 – 429,519
Length	110
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	94.78
Mean single sequence MFE	-28.56
Consensus MFE	-28.40
Energy contribution	-29.20
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.03
Structure conservation index	0.99
SVM decision value	0.20
SVM RNA-class probability	0.632548
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 429409 110 - 22407834
--------AAAAGAACGGCCAAAAAUGUUUUAUGCAAUUCCUUGAAGUCGAUUUCAGUCUCCAGUCUCCCGGUCCAGAGAAUCGCUUUUGCGGAAUUGGCGCGCAUUUCUGGCCUUUU
--------........(((((.((((((....(((((((((..((((.((((((......((........))......))))))))))...)))))).))).)))))).))))).... ( -32.60)
>DroSec_CAF1 6920 110 - 1
--------AAAAGAACGGCCAAAAAUGUUUUAUGCAAUUCCUUGAAGUCGAUUUCAGUCUCCAGUCUCCCGGUCCAGAGAAUCGCUUUUGCGGAAUUGGCGCGCAUUUCUGGCCUUUU
--------........(((((.((((((....(((((((((..((((.((((((......((........))......))))))))))...)))))).))).)))))).))))).... ( -32.60)
>DroSim_CAF1 5907 110 - 1
--------AAAAGAACGGCCAAAAAUGUUUUAUGCAAUUCCUUGAAGUCGAUUUCAGUCUCCAGUCUCCCGGUCCAGAGAAUCGCUUUUGCGGAAUUGGCGCGCAUUUCUGGCCUUUU
--------........(((((.((((((....(((((((((..((((.((((((......((........))......))))))))))...)))))).))).)))))).))))).... ( -32.60)
>DroEre_CAF1 6654 114 - 1
--AAAUAAAAAAGAACGACCAAAAAUGUUUUAUGCAAUUCCUUGAAGUCGAUUUCAGUCUCCAGUCUCCCGGUCCAGAGAAUCGCUUUUGCGGAAUUGGCGCGCAU-UCUGGCCUUU-
--..............(.(((..(((((....(((((((((..((((.((((((......((........))......))))))))))...)))))).))).))))-).))).)...- ( -22.50)
>DroYak_CAF1 6278 117 - 1
AAAAAUAAAAAAGAACGACCAAAAAUGUUUUAUGCAAUUCCUUGAAGUCGAUUUCAGUCUCCAGUCUCCCGGUCCAGAGAAUCGCUUUUGCGGAAUUGGCGCGCAU-UCUGGCCUUUU
................(.(((..(((((....(((((((((..((((.((((((......((........))......))))))))))...)))))).))).))))-).))).).... ( -22.50)
>consensus
________AAAAGAACGGCCAAAAAUGUUUUAUGCAAUUCCUUGAAGUCGAUUUCAGUCUCCAGUCUCCCGGUCCAGAGAAUCGCUUUUGCGGAAUUGGCGCGCAUUUCUGGCCUUUU
................(((((.((((((....(((((((((..((((.((((((......((........))......))))))))))...)))))).))).)))))).))))).... (-28.40 = -29.20 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:13 2006