Locus 437

Sequence ID	X_DroMel_CAF1
Location	1,281,859 – 1,281,965
Length	106
Max. P	0.877535

overview

Window 2

Location	1,281,859 – 1,281,965
Length	106
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	85.67
Mean single sequence MFE	-42.62
Consensus MFE	-30.14
Energy contribution	-33.20
Covariance contribution	3.06
Combinations/Pair	1.11
Mean z-score	-2.20
Structure conservation index	0.71
SVM decision value	0.90
SVM RNA-class probability	0.877535
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1281859 106 + 22224390
CCGCCCCUCCAACAGUUGCACUUUCUGCCACCCUCUUUCCGAAUCUGAACCAGAGUCUGGAGUCUGGAGGGUGGAUGGUGGAGGGCAAAUAGUGGCGGAGGGACUG
....((((((..((.((((.(((((..(((((((((((((((.((((...)))).)).))))...))))))))).....)))))))))....))..)))))).... ( -46.80)
>DroSec_CAF1 14585 106 + 1
CCGCCCCUCCAACAGUUGCACUUUCUGCCGCCCUCUUUCCGAAUCUGAACCAGAGUCUGGAGUCUGGAGGGUGGAUGGUGGAGGGCAGAUAGUGGCGUAGGGACUG
....(((((((....((((.(((((..(((((((((((((((.((((...)))).)).))))...))))))))).....)))))))))....)))...)))).... ( -42.20)
>DroSim_CAF1 12135 105 + 1
CGGCCCCUCCAACAGUUGCACUUUCUGCCGCCCUCUUUCCAAAUCUGAACCAGAGUCUGGAGUCUGGAGGGUAGA-GUUGGAGGGCAGAUAGUGGCGGAGGGACUG
(((.((((((..(....)((((.((((((((((((((((((..((((...))))...)))))...)))))))...-.......)))))).))))..)))))).))) ( -44.50)
>DroEre_CAF1 16337 92 + 1
-UGCCCCUCCAACAGUUGCACUUUCAGCCGCCCUCUUACCGAAUCUGAACCAGAGUCUCGAGUCUGGAGGGUGGC-GGUGGAA------------CUACGGAACUG
-......(((...((((.((((....((((((((((.(((((.((((...))))...))).))..))))))))))-)))).))------------))..))).... ( -37.00)
>consensus
CCGCCCCUCCAACAGUUGCACUUUCUGCCGCCCUCUUUCCGAAUCUGAACCAGAGUCUGGAGUCUGGAGGGUGGA_GGUGGAGGGCAGAUAGUGGCGGAGGGACUG
....((((((..((.((((.(((((..((((((((((((((..((((...))))...)))))...))))))))).....)))))))))....))..)))))).... (-30.14 = -33.20 +   3.06)

alignment

secondary structure

dotplot

Window 3

Location	1,281,859 – 1,281,965
Length	106
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	85.67
Mean single sequence MFE	-38.03
Consensus MFE	-27.67
Energy contribution	-29.91
Covariance contribution	2.25
Combinations/Pair	1.17
Mean z-score	-1.86
Structure conservation index	0.73
SVM decision value	0.55
SVM RNA-class probability	0.780038
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1281859 106 - 22224390
CAGUCCCUCCGCCACUAUUUGCCCUCCACCAUCCACCCUCCAGACUCCAGACUCUGGUUCAGAUUCGGAAAGAGGGUGGCAGAAAGUGCAACUGUUGGAGGGGCGG
..(((((((((.((....((((.((.......((((((((.....(((.((.((((...)))).)))))..)))))))).....)).)))).)).))))))))).. ( -41.80)
>DroSec_CAF1 14585 106 - 1
CAGUCCCUACGCCACUAUCUGCCCUCCACCAUCCACCCUCCAGACUCCAGACUCUGGUUCAGAUUCGGAAAGAGGGCGGCAGAAAGUGCAACUGUUGGAGGGGCGG
..((((((..((((((.((((((.(((.(..(((.....(((((........))))).........)))..).))).)))))).)))).....))...)))))).. ( -35.94)
>DroSim_CAF1 12135 105 - 1
CAGUCCCUCCGCCACUAUCUGCCCUCCAAC-UCUACCCUCCAGACUCCAGACUCUGGUUCAGAUUUGGAAAGAGGGCGGCAGAAAGUGCAACUGUUGGAGGGGCCG
..((((((((((((((.((((((.......-....(((((.....((((((.((((...))))))))))..))))).)))))).)))).....).))))))))).. ( -42.40)
>DroEre_CAF1 16337 92 - 1
CAGUUCCGUAG------------UUCCACC-GCCACCCUCCAGACUCGAGACUCUGGUUCAGAUUCGGUAAGAGGGCGGCUGAAAGUGCAACUGUUGGAGGGGCA-
..(((((.(((------------((.(((.-(((.(((((...((.((((..((((...))))))))))..))))).))).....))).))))).....))))).- ( -32.00)
>consensus
CAGUCCCUCCGCCACUAUCUGCCCUCCACC_UCCACCCUCCAGACUCCAGACUCUGGUUCAGAUUCGGAAAGAGGGCGGCAGAAAGUGCAACUGUUGGAGGGGCGG
..(((((((((.((((.((((((.(((....(((.....(((((........))))).........)))....))).)))))).)))).......))))))))).. (-27.67 = -29.91 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:34 2006