Locus 2350

Sequence ID	2L_DroMel_CAF1
Location	6,367,713 – 6,367,864
Length	151
Max. P	0.942754

overview

Window 1

Location	6,367,713 – 6,367,825
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.16
Mean single sequence MFE	-38.22
Consensus MFE	-30.48
Energy contribution	-30.85
Covariance contribution	0.37
Combinations/Pair	1.07
Mean z-score	-2.50
Structure conservation index	0.80
SVM decision value	1.33
SVM RNA-class probability	0.942754
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6367713 112 + 22407834
GCCGAGCUGCAAGAAUUCUACAAGCACAGUCGUCGGAAGAAACCCCGCAAGUGGGGUAGUGUGGGUAAUAAUAUUUGGUGUAGCGGCGAUGAGAGAGCACAAAUGC-GAAU-------AC
(((..((((((.((((..(((..((((.....((....)).((((((....)))))).))))..))).....))))..))))))))).........(((....)))-....-------.. ( -35.60)
>DroSec_CAF1 12813 109 + 1
GCCGAGCUGCAAGAAUUCUACAAGCUCAGUCGUCGGAAGAAACCCCUCAAGUGGGGUAGUGUGGGUAA---UAUUUGGUGUAGCGGCGAUGAGAGAGCACAAAUGC-GAAU-------AC
(((..((((((.((((..(((..((.(.....((....)).(((((......))))).).))..))).---.))))..))))))))).........(((....)))-....-------.. ( -33.50)
>DroEre_CAF1 12652 116 + 1
GCCGAGCUGCAAGAAUUCUACAAGCACAGUCGUCGGAAGAAACCCCGCAAGUGAGGUAGUGUGGGUAA---UAUUCGGUGUAGUGGCGGUGAGAGCGCACAAAUGC-AAAUACGGCAAAC
((((.((((((.((((..(((..((((.....((....)).(((((....).).))).))))..))).---.))))..)))))).(((.(....))))........-.....)))).... ( -38.50)
>DroYak_CAF1 12916 117 + 1
GCCGAGCUGCAAGAAUUCUACAAGCACAGUCGUCGGAAGAAACCCCGCAAGUGGGGUAGUGUGGGUAA---UAUUUGGUGUAGCGGCGAUGAGAGAGCUCAAAUGCGAAAUACGGCAUAC
((((.((((((.((((..(((..((((.....((....)).((((((....)))))).))))..))).---.))))..)))))).(((.((((....))))..)))......)))).... ( -45.30)
>consensus
GCCGAGCUGCAAGAAUUCUACAAGCACAGUCGUCGGAAGAAACCCCGCAAGUGGGGUAGUGUGGGUAA___UAUUUGGUGUAGCGGCGAUGAGAGAGCACAAAUGC_AAAU_______AC
(((..((((((.((((..(((..((((.....((....)).((((((....)))))).))))..))).....))))..))))))))).........((......)).............. (-30.48 = -30.85 +   0.37)

alignment

secondary structure

dotplot

Window 2

Location	6,367,753 – 6,367,864
Length	111
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	89.64
Mean single sequence MFE	-29.98
Consensus MFE	-23.26
Energy contribution	-23.39
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-1.95
Structure conservation index	0.78
SVM decision value	0.65
SVM RNA-class probability	0.811049
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6367753 111 + 22407834
AACCCCGCAAGUGGGGUAGUGUGGGUAAUAAUAUUUGGUGUAGCGGCGAUGAGAGAGCACAAAUGC-GAAU-------ACGGCAUACGACAUACGGAAUAUAUGUACAUAAAAUCGAAA
.((((((....)))))).(((((.(((....(((((.((((..((((..(....).))....((((-....-------...)))).))..)))).)))))))).))))).......... ( -28.50)
>DroSec_CAF1 12853 107 + 1
AACCCCUCAAGUGGGGUAGUGUGGGUAA---UAUUUGGUGUAGCGGCGAUGAGAGAGCACAAAUGC-GAAU-------ACGGCAUACGACAUACGGAAUAUAUGUACAUAA-AUCGAAA
.(((((......))))).(((((.(((.---(((((.((((..((((..(....).))....((((-....-------...)))).))..)))).)))))))).)))))..-....... ( -29.70)
>DroEre_CAF1 12692 115 + 1
AACCCCGCAAGUGAGGUAGUGUGGGUAA---UAUUCGGUGUAGUGGCGGUGAGAGCGCACAAAUGC-AAAUACGGCAAACGGCAUACGGCAUACGGAAUAUAUGUACAUAAAAUCGAAA
.(((((....).).))).(((((.(((.---(((((.((((.(((.((((....))(((....)))-.....)).)...((.....)))))))).)))))))).))))).......... ( -29.00)
>DroYak_CAF1 12956 116 + 1
AACCCCGCAAGUGGGGUAGUGUGGGUAA---UAUUUGGUGUAGCGGCGAUGAGAGAGCUCAAAUGCGAAAUACGGCAUACGGCAUACGACAUACGGAAUAUAUGUACAUAAAAUCGAAA
.((((((....)))))).(((((.(((.---(((((.((((..((((..((((....)))).((((........))))...))...))..)))).)))))))).))))).......... ( -32.70)
>consensus
AACCCCGCAAGUGGGGUAGUGUGGGUAA___UAUUUGGUGUAGCGGCGAUGAGAGAGCACAAAUGC_AAAU_______ACGGCAUACGACAUACGGAAUAUAUGUACAUAAAAUCGAAA
.((((((....)))))).(((((.(((....(((((.((((..((((.........))....((((...............)))).))..)))).)))))))).))))).......... (-23.26 = -23.39 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:59 2006