Locus 7249

Sequence ID	X_DroMel_CAF1
Location	18,090,839 – 18,090,998
Length	159
Max. P	0.929747

overview

Window 6

Location	18,090,839 – 18,090,958
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-39.35
Consensus MFE	-36.08
Energy contribution	-37.32
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.92
SVM decision value	1.08
SVM RNA-class probability	0.912303
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18090839 119 - 22224390
AACAAUAAAAAACAAUCCGCUGCC-CCACCGCCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUGCGCACAAGACGCACCAGAGAUGGAUAUGGCAGCGAUCCCA
.................(((((((-...((((......)))).(((((((......((((.(((.......)))))))(((((....).)))).....)))))))..)))))))...... ( -42.60)
>DroSec_CAF1 13186 120 - 1
AACAAUAAAAAACAAUCCGCUGCCCCCACCGCCCCCUCGAGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUGCGCACAAGACGCACCAGAGAUGGAUAUGGCAGCGAUCCCA
.................(((((((..........((....)).(((((((......((((.(((.......)))))))(((((....).)))).....)))))))..)))))))...... ( -37.20)
>DroEre_CAF1 10350 119 - 1
AACAAUAAAAAACAAUCCGCUGCCCCCACCGCCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUGCGCACAAGACGCACCAGAGAUGGAUAUGGCAGCGAUCCC-
.................(((((((....((((......)))).(((((((......((((.(((.......)))))))(((((....).)))).....)))))))..))))))).....- ( -42.60)
>DroYak_CAF1 12348 114 - 1
AACAAUAAAAAACAAUCCGCCGCCGC-----CCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUGCGCACAAGACGCACCAGAGAUGGAUAUGGCAGCGAUCCC-
.............(((((((.(((((-----.......)).((((.......)))))))..)))))))...(((.((((((((....).))))(((....)))....))).))).....- ( -35.00)
>consensus
AACAAUAAAAAACAAUCCGCUGCCCCCACCGCCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUGCGCACAAGACGCACCAGAGAUGGAUAUGGCAGCGAUCCC_
.................(((((((....((((......)))).(((((((......((((.(((.......)))))))(((((....).)))).....)))))))..)))))))...... (-36.08 = -37.32 +   1.25)

alignment

secondary structure

dotplot

Window 7

Location	18,090,879 – 18,090,998
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.39
Mean single sequence MFE	-37.75
Consensus MFE	-34.35
Energy contribution	-35.35
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.30
Structure conservation index	0.91
SVM decision value	1.20
SVM RNA-class probability	0.929747
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18090879 119 - 22224390
GCGCGGACAGCGCGAAAUAAAAGCGCAGAAAUGUUAAAUAAACAAUAAAAAACAAUCCGCUGCC-CCACCGCCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUG
((((.....)))).........((((.....((((.....)))).........(((((((((((-....(((......)))((((.......)))))).)))))))))..))))...... ( -39.80)
>DroSec_CAF1 13226 120 - 1
GCGCGGACAGCGCGAAAUAAAAGCGCAGAAAUGUUAAAUAAACAAUAAAAAACAAUCCGCUGCCCCCACCGCCCCCUCGAGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUG
((((.....)))).........((((.....((((.....)))).........(((((((((((.....((......))..((((.......)))))).)))))))))..))))...... ( -35.80)
>DroEre_CAF1 10389 120 - 1
GCGCGGACAGCGCGAAAUAAAAGCGCAGAAAUGUUAAAUAAACAAUAAAAAACAAUCCGCUGCCCCCACCGCCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUG
((((.....)))).........((((.....((((.....)))).........(((((((((((.....(((......)))((((.......)))))).)))))))))..))))...... ( -39.80)
>DroYak_CAF1 12387 115 - 1
GCGCGGACAGCGCGAAAUAAAAGCGCAGAAAUGUUAAAUAAACAAUAAAAAACAAUCCGCCGCCGC-----CCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUG
((((.....)))).........((((.....((((.....)))).........(((((((.(((((-----.......)).((((.......)))))))..)))))))..))))...... ( -35.60)
>consensus
GCGCGGACAGCGCGAAAUAAAAGCGCAGAAAUGUUAAAUAAACAAUAAAAAACAAUCCGCUGCCCCCACCGCCCCCUCGCGGAGUCUGUCAAACUCGGCCAGCGGAUUAAGCGCGGCCUG
((((.....)))).........((((.....((((.....)))).........(((((((((((.....(((......)))((((.......)))))).)))))))))..))))...... (-34.35 = -35.35 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:09 2006