Locus 2185

Sequence ID	2L_DroMel_CAF1
Location	5,909,317 – 5,909,462
Length	145
Max. P	0.578342

overview

Window 5

Location	5,909,317 – 5,909,427
Length	110
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	92.12
Mean single sequence MFE	-42.20
Consensus MFE	-36.78
Energy contribution	-37.52
Covariance contribution	0.75
Combinations/Pair	1.13
Mean z-score	-1.42
Structure conservation index	0.87
SVM decision value	0.09
SVM RNA-class probability	0.578342
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5909317 110 + 22407834
GGGUUUCAUUGUGGCCUCGCUGUUCUCACUUGACCGAGUUGAAACAAGGCUAACAGUGCUCCUGUCCUCGAUUUUGGCCCACAAGCUCGAGGAAUCGCUGGAGCCGCGCC
.(((...((((((((((...((((.((((((....))).)))))))))))).)))))(((((..(((((((.((((.....)))).)))))))......)))))...))) ( -38.50)
>DroSec_CAF1 99754 110 + 1
GGGUUUCACUGUGGCCUCGCUGCUCUCACUUGACCGAUUUGAAACGAUGCUCACAGUGCUCCUGUCCUCGAUUUUGGCCCACAAGCUCGAGGAAUCGCUGGAGCCGCGCC
.(((...((((((((.(((...(..((........))...)...))).)).))))))(((((..(((((((.((((.....)))).)))))))......)))))...))) ( -36.50)
>DroEre_CAF1 124477 110 + 1
GGGUUUCACUGUGGCCUCGCUGUUCUGACUCGACCGAGUUGACACGAGGCUAGCAGUGCUUCUGUCCUCGAUUUUGGCCCACAAGCUGGAGGAAUCGCUGGAGCCGCGCC
.((((((((((((((((((.((((..(((((....))))))))))))))))).))))((.....(((((.(.((((.....)))).).)))))...)).))))))..... ( -46.20)
>DroYak_CAF1 125556 110 + 1
GGGUUUCACUGUGGCCUCGCUGCUCUGACUCGACCGAUUUGAAGCGAGGCUUACAGUGCUUCUGUCCUCGAUCUUGGCCCACAGGCUCGAGGAAUCGCUGGAGCCGCGCC
.((((((((((((((((((((..((.((.((....)))).)))))))))).))))))((.....(((((((.((((.....)))).)))))))...)).))))))..... ( -47.60)
>consensus
GGGUUUCACUGUGGCCUCGCUGCUCUCACUCGACCGAGUUGAAACGAGGCUAACAGUGCUCCUGUCCUCGAUUUUGGCCCACAAGCUCGAGGAAUCGCUGGAGCCGCGCC
.((((((((((((((((((....((.(((((....)))))))..))))))).)))))((.....(((((((.((((.....)))).)))))))...)).))))))..... (-36.78 = -37.52 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	5,909,347 – 5,909,462
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	68.69
Mean single sequence MFE	-41.38
Consensus MFE	-20.73
Energy contribution	-19.38
Covariance contribution	-1.36
Combinations/Pair	1.40
Mean z-score	-1.43
Structure conservation index	0.50
SVM decision value	0.00
SVM RNA-class probability	0.535374
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5909347 115 + 22407834
UGACCGAGUUGAAACAAGGCUAACAGUGCUCCUGUCCUCGAUUUUGGCCCACAAGCUCGAGGAAUCGCUGGAGCCGCGCCAGGCUGAAGCAGACCUGCGCAUCUUAUUGGC--CU---GC
................(((((((..(.(((((..(((((((.((((.....)))).)))))))......))))))((((.((((((...))).)))))))......)))))--))---.. ( -45.10)
>DroPse_CAF1 206767 93 + 1
----------------------GGAGUACUCCAGUCCUCGAUCUUUGCCCAAAGGCUAGAGGAAUCGCUUGAGCCACGCCAUGUCCAGGA--GUCCCUGUGGCGUGUGCGUCCCU---CA
----------------------(((....)))..(((((..(((((....)))))...)))))......((((..((((((((((((((.--...)))).)))))).))))..))---)) ( -36.50)
>DroSec_CAF1 99784 115 + 1
UGACCGAUUUGAAACGAUGCUCACAGUGCUCCUGUCCUCGAUUUUGGCCCACAAGCUCGAGGAAUCGCUGGAGCCGCGCCAGACUGAAGCUGAUCGGCGCAGCUUAUUGGC--CU---GC
...(((((..(.......((((.(((((......(((((((.((((.....)))).)))))))..))))))))).(((((.(((.......).)))))))..)..))))).--..---.. ( -40.50)
>DroEre_CAF1 124507 115 + 1
CGACCGAGUUGACACGAGGCUAGCAGUGCUUCUGUCCUCGAUUUUGGCCCACAAGCUGGAGGAAUCGCUGGAGCCGCGCCAGGCUGAAGCAGAUCGGCGUGGCAUAUUAGG--CU---CC
(((.((((..((((.(((((.......))))))))))))).(((..((......))..)))...)))..((((((..((((.(((((......))))).))))......))--))---)) ( -46.30)
>DroYak_CAF1 125586 115 + 1
CGACCGAUUUGAAGCGAGGCUUACAGUGCUUCUGUCCUCGAUCUUGGCCCACAGGCUCGAGGAAUCGCUGGAGCCGCGCCAGGCUGAGGCAGAUCGUCGUGGUUUAUUAGG--CU---CC
............((((((((.......)))))..(((((((.((((.....)))).)))))))...)))((((((..((((.(.(((......))).).))))......))--))---)) ( -43.40)
>DroPer_CAF1 206709 96 + 1
----------------------GGAGUACUCCAGUCCUCGAUCUUUGCCCAAAGGCUAGAGGAAUCGCUUGAGCCACGCCAUGUCCAGGA--GUCCCUGUGGCGUGUGCGUCCCUCUCCA
----------------------((((..(((.(((((((..(((((....)))))...))))....))).)))..((((((((((((((.--...)))).)))))).))))....)))). ( -36.50)
>consensus
_GACCGA_UUGAAACGAGGCU_ACAGUGCUCCUGUCCUCGAUCUUGGCCCACAAGCUCGAGGAAUCGCUGGAGCCGCGCCAGGCUGAAGCAGAUCGGCGUGGCUUAUUAGC__CU___CC
.......................(((((......(((((...((((.....))))...)))))..)))))..((((((...................))))))................. (-20.73 = -19.38 +  -1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:44 2006