Locus 3619

Sequence ID	2L_DroMel_CAF1
Location	10,554,003 – 10,554,133
Length	130
Max. P	0.823538

overview

Window 2

Location	10,554,003 – 10,554,112
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.07
Mean single sequence MFE	-30.08
Consensus MFE	-24.11
Energy contribution	-23.78
Covariance contribution	-0.33
Combinations/Pair	1.20
Mean z-score	-1.54
Structure conservation index	0.80
SVM decision value	0.03
SVM RNA-class probability	0.546385
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10554003 109 - 22407834
-AUUGGC---CCACAUUCACAUGCCACACACGCAGCCGGCGAAGAAAUUUAAAACGUCAACAAGACCGUUGACAGUUGGCGCUGUGCAGGACUCGUAAAAAA-----CUGCG--UCACUC
-..((((---............)))).(((.((.(((((((((....))).....((((((......)))))).)))))))))))((((.............-----)))).--...... ( -29.62)
>DroPse_CAF1 44578 118 - 1
GACCGACCUUUCGCGUUCGCAUGCCACACACGCAGCCUGCAAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGCGCUGUGCAGGAAUCGUAAAAAAAAACCCCCCG--CCACAU
...((((((...((....))......((((.((.(((.(((((....))).....((((((......)))))).)).))))))))).)))..))).................--...... ( -25.60)
>DroEre_CAF1 42410 109 - 1
-AUUGGC---CCACAUUCACGUGCCACACACGCAGCCAGCGGAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGCGCUGUGCAGGACUCGUAAAAAA-----CCGCG--CCACUC
-..((((---(.......(((.(((.((((.((.(((((((((....))).....((((((......)))))).))))))))))))..)).).)))......-----..).)--)))... ( -33.66)
>DroYak_CAF1 43730 109 - 1
-AGUGGC---CCACAUUCACGUGCCACACACGCAGCCAGCGAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGCGCUGUGCAGGACUCGUAAAAAA-----CUGCG--CCACUC
-((((((---.((.....(((.(((.((((.((.(((((((((....))).....((((((......)))))).))))))))))))..)).).)))......-----.)).)--))))). ( -38.90)
>DroAna_CAF1 46478 111 - 1
-ACAACC---UCGCACUCACAUGCCGCACACGCAGCUAGCAAAGAAAUUUAAAACGUCAACAAGCCCAUUGACAGUUGGCGCUGUGCAGGACUCGUAAAAAA-----AGGCUGCCCCCUC
-....((---(.(((......))).(((((.((.(((((((((....))).....(((((........))))).))))))))))))))))............-----(((......))). ( -27.10)
>DroPer_CAF1 44563 118 - 1
GACCGACCUUUCGCGUUCGCAUGCCACACACGCAGCCUGCAAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGCGCUGUGCAGGAAUCGUAAAAAAAAACCCCCCG--CCACAU
...((((((...((....))......((((.((.(((.(((((....))).....((((((......)))))).)).))))))))).)))..))).................--...... ( -25.60)
>consensus
_ACUGGC___CCACAUUCACAUGCCACACACGCAGCCAGCAAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGCGCUGUGCAGGACUCGUAAAAAA_____CCGCG__CCACUC
..................((...((.((((.((.(((((((((....))).....((((((......)))))).))))))))))))..))....))........................ (-24.11 = -23.78 +  -0.33)

alignment

secondary structure

dotplot

Window 3

Location	10,554,036 – 10,554,133
Length	97
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.74
Mean single sequence MFE	-20.29
Consensus MFE	-17.37
Energy contribution	-17.23
Covariance contribution	-0.14
Combinations/Pair	1.26
Mean z-score	-1.48
Structure conservation index	0.86
SVM decision value	0.69
SVM RNA-class probability	0.823538
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10554036 97 - 22407834
CCA-CUC------CAUGCCCCCA------------ACCCA-AUUGGCCCACAUUCACAUGCCACACACGCAGCCGGCGAAGAAAUUUAAAACGUCAACAAGACCGUUGACAGUUGGC
...-...------..........------------.....-..((((............))))........(((((((((....))).....((((((......)))))).)))))) ( -19.80)
>DroSec_CAF1 41818 98 - 1
CCA-CUC------CAUGCCCCCU------------CCCAAAAUUGGCCCACAUUCACAUGCCACACACGCAGUCGGCGAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGC
(((-.((------..((((..((------------........((((............)))).......))..))))..))..........((((((......))))))...))). ( -18.16)
>DroSim_CAF1 41464 98 - 1
CCA-CUC------CAUGCCCCCU------------CCCAAACUUGGCCCACAUUCACAUGCCACACACGCAGCCGGCGAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGC
...-...------..........------------........((((............))))........(((((((((....))).....((((((......)))))).)))))) ( -19.80)
>DroEre_CAF1 42443 94 - 1
CCA-CUC------CAUUCCCGCU------------CC----AUUGGCCCACAUUCACGUGCCACACACGCAGCCAGCGGAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGC
...-..(------((......((------------((----.(((((.........((((.....))))..))))).))))...........((((((......))))))...))). ( -23.50)
>DroYak_CAF1 43763 113 - 1
CCAUCUCCAUCCCCAUUCCCAUUCCAAGCCUGCUCCC----AGUGGCCCACAUUCACGUGCCACACACGCAGCCAGCGAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGC
..............................(((....----.(((((.(........).)))))....)))(((((((((....))).....((((((......)))))).)))))) ( -26.90)
>DroAna_CAF1 46513 84 - 1
CCG-CAC----------------------------CC----ACAACCUCGCACUCACAUGCCGCACACGCAGCUAGCAAAGAAAUUUAAAACGUCAACAAGCCCAUUGACAGUUGGC
...-...----------------------------..----........(((......))).((....)).(((((((((....))).....(((((........))))).)))))) ( -13.60)
>consensus
CCA_CUC______CAUGCCCCCU____________CC____AUUGGCCCACAUUCACAUGCCACACACGCAGCCAGCGAAGAAAUUUAAAACGUCAACAAGCCCGUUGACAGUUGGC
...........................................((((............))))........(((((((((....))).....((((((......)))))).)))))) (-17.37 = -17.23 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:02 2006