Locus 3424

Sequence ID	2L_DroMel_CAF1
Location	9,924,691 – 9,924,827
Length	136
Max. P	0.953471

overview

Window 3

Location	9,924,691 – 9,924,807
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.66
Mean single sequence MFE	-41.87
Consensus MFE	-26.51
Energy contribution	-25.22
Covariance contribution	-1.30
Combinations/Pair	1.45
Mean z-score	-1.39
Structure conservation index	0.63
SVM decision value	0.02
SVM RNA-class probability	0.542877
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9924691 116 - 22407834
AGAGGAGCCCCUAAGAGGUUUCCUGGAGGAGAUCAACUGCCCGGAACCGGGCAUCAUAGAUCGUCAGAUGAUCGAAACUGCUUAUUUGGAGGAGGGCAAGAAGGGCGAGGCGAGAA
......(((((((.(((((((((....)))))))...((((((....)))))))).))).((..(((((((.((....)).)))))))..)).))))................... ( -36.90)
>DroPse_CAF1 1791 116 - 1
GGAGGAGCCGGUGAGGGGCUUCCUGGAGGAGGUCAACUGCCCAGAGCCGGGCAUCAUUGAUCGGCAGAUGAUCGAGACCGCCUACCUGGGGGAGGGACAAAAGGGCGAGUCGGGUC
......((((((.((.(((((((....)))))))...(((((......)))))...)).))))))....((((..((((((((.(((.....))).......))))).))).)))) ( -44.90)
>DroEre_CAF1 1890 116 - 1
GGAGGAGCCCCUGAGGGGCUUCCUGGAGGAGAUCAACUGCCCGGAACCGGGCAUCAUAGAUCGUCGGAUGAUUGAAACCGCCUAUCUGGAGGAGGGCCAAAAGGGCGAGGCGAGAA
((.((((((((...))))))))((((....((((...((((((....)))))).....)))).))))..........))((((.(((.....)))(((.....))).))))..... ( -44.10)
>DroWil_CAF1 2116 115 - 1
-UAUGAGGCCACCAAGGGUUUUCUGGAGGAGAUUAAUUGCCCAGAGCCAGGCAUCAUUGAUCGGGAGAUGAUUGAGUCUGCGUAUCUGGAGGAAGGCCCAAAAGGAGAAGCCAAAC
-.....(((..((..((((((((((.((........)).)((((((((((((.(((.(.(((....))).).)))))))).)).))))).)))))))))....))....))).... ( -37.00)
>DroAna_CAF1 3128 116 - 1
GGGGGAGCCGGCAAAGGACUUUCUCCAGGAGAUCAACUGCCCAGAGCCGGGCAUCAUUGAUCGGAAAAUGAUCGAAACCGCUUACCUGGAGGAGGGCCAGAAGGGUGAAUCCAAGC
(((...(((......((.(((((((((((.((((((.(((((......)))))...))))))......(((.((....)).)))))))))))))).)).....)))...))).... ( -43.40)
>DroPer_CAF1 1791 116 - 1
GGAGGAGCCGGUGAGGGGCUUCCUGGAGGAGGUCAACUGCCCAGAGCCGGGCAUCAUUGAUCGGCAGAUGAUCGAGACCGCCUACCUGGGGGAGGGACAAAAGGGCGAGUCGGGUC
......((((((.((.(((((((....)))))))...(((((......)))))...)).))))))....((((..((((((((.(((.....))).......))))).))).)))) ( -44.90)
>consensus
GGAGGAGCCCGUGAGGGGCUUCCUGGAGGAGAUCAACUGCCCAGAGCCGGGCAUCAUUGAUCGGCAGAUGAUCGAAACCGCCUACCUGGAGGAGGGCCAAAAGGGCGAGGCGAGAC
......(((.......(((((((....)))))))..((.(((((.(..((((....(((((((.....)))))))....)))).))))).).)).........))).......... (-26.51 = -25.22 +  -1.30)

alignment

secondary structure

dotplot

Window 4

Location	9,924,731 – 9,924,827
Length	96
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.53
Mean single sequence MFE	-26.48
Consensus MFE	-18.34
Energy contribution	-18.95
Covariance contribution	0.61
Combinations/Pair	1.12
Mean z-score	-1.73
Structure conservation index	0.69
SVM decision value	1.43
SVM RNA-class probability	0.953471
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9924731 96 + 22407834
UUCGAUCAUCUGACGAUCUAUGAUGCCCGGUUCCGGGCAGUUGAUCUCCUCCAGGAAACCUCUUAGGGGCUCCUCUUCCGUCUCCU---C---------CACAGCAUC
...........(((((((.....((((((....))))))...))))......((((..(((....)))..)))).....)))....---.---------......... ( -27.90)
>DroPse_CAF1 1831 92 + 1
CUCGAUCAUCUGCCGAUCAAUGAUGCCCGGCUCUGGGCAGUUGACCUCCUCCAGGAAGCCCCUCACCGGCUCCUCCAU---CUCAU---C---------CCCCGAAC-
...(((.....((((.(((((..((((((....)))))))))))..(((....)))..........))))......))---)....---.---------........- ( -22.30)
>DroSec_CAF1 1934 105 + 1
UUCGAUCAUCUGACGAUCUAUGAUGCCCGGUUCCGGGCAGUUGAUCUCCUCCAGGAAACCCAUUAGGGGCUCCUCCUCCGCCUCCU---CCUCCUUUUCCGUAGCACU
............((((((.....((((((....))))))...)))).......(((((......((((((.........))).)))---......)))))))...... ( -29.10)
>DroEre_CAF1 1930 102 + 1
UUCAAUCAUCCGACGAUCUAUGAUGCCCGGUUCCGGGCAGUUGAUCUCCUCCAGGAAGCCCCUCAGGGGCUCCUCCUCCGCCUCCU------UCUCCUCCGCAGCACU
...........((.((((.....((((((....))))))...))))))....((((.(((((...)))))))))............------................ ( -30.90)
>DroAna_CAF1 3168 108 + 1
UUCGAUCAUUUUCCGAUCAAUGAUGCCCGGCUCUGGGCAGUUGAUCUCCUGGAGAAAGUCCUUUGCCGGCUCCCCCUCCUCCUCCAACUCCUCGACUCCCGCCUCACU
.((((.........(((((((..((((((....)))))))))))))....((((..((((.......))))....))))............))))............. ( -26.40)
>DroPer_CAF1 1831 92 + 1
CUCGAUCAUCUGCCGAUCAAUGAUGCCCGGCUCUGGGCAGUUGACCUCCUCCAGGAAGCCCCUCACCGGCUCCUCCAU---CUCAU---C---------CCCCGAAC-
...(((.....((((.(((((..((((((....)))))))))))..(((....)))..........))))......))---)....---.---------........- ( -22.30)
>consensus
UUCGAUCAUCUGACGAUCAAUGAUGCCCGGCUCCGGGCAGUUGAUCUCCUCCAGGAAGCCCCUCACCGGCUCCUCCUCCGCCUCCU___C_________CGCAGCACU
..............((((.....((((((....))))))...))))......((((.(((.......))))))).................................. (-18.34 = -18.95 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:14 2006