Locus 872

Sequence ID	2R_DroMel_CAF1
Location	4,025,025 – 4,025,264
Length	239
Max. P	0.876938

overview

Window 9

Location	4,025,025 – 4,025,144
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.13
Mean single sequence MFE	-33.80
Consensus MFE	-27.26
Energy contribution	-27.70
Covariance contribution	0.44
Combinations/Pair	1.12
Mean z-score	-1.78
Structure conservation index	0.81
SVM decision value	0.90
SVM RNA-class probability	0.876938
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4025025 119 - 20766785
GCGCAACUUUUGCCAACUGUGCGAAAGUU-UUUUUAUGGCGCCGCGAACAAGCGGUCAGCGAUUUAAUUUUAAUUGUAUUUAGAUAAGAUUUAAUGGCGUUUGUUCUAGAGCAGAGCGCA
((((((((((((((....).)))))))))-.(((((..(((((((......)))))..((.(((.(((((((.(((....))).))))))).))).))....))..)))))....)))). ( -36.10)
>DroSec_CAF1 7828 119 - 1
GCGCAACUUUUGCCAACUGUGCGAAAGUU-UUUUUAUGGCGCCGCGGACAAGUGGUCAGCGAUUUAAUUUUAAUUGUAUUUAGAUAAGAUUUAAUGGCGUUUGUUCUGGAGCAGAGCGCA
((((((((((((((....).)))))))))-........((.(((.(((((((......((.(((.(((((((.(((....))).))))))).))).)).)))))))))).))...)))). ( -35.50)
>DroSim_CAF1 9878 119 - 1
GCGCAACUUUUGCCAACUGUGCGAAAGUU-UUUUUAUGGCGCCGCGGACAAGUGGUCAGCGAUUUAAUUUUAAUUGUAUUUAGAUAAGAUUUAAUGGCGUUUGUUCUGGAGCAGAGCGCA
((((((((((((((....).)))))))))-........((.(((.(((((((......((.(((.(((((((.(((....))).))))))).))).)).)))))))))).))...)))). ( -35.50)
>DroEre_CAF1 7080 111 - 1
GCGCAACUUUUGCCAACUGUGCGAAAGUUGUUUUUACGGCGCCGCGGCCAAGUGGUCAGCGAUUUAAUUUUAAUUGUAUUUAGAUAAGACUUAAUGGUGUUUGUGCUGGAG---------
..((((((((((((....).))))))))))).....(((((((((((((....)))).))).........................((((........))))))))))...--------- ( -32.40)
>DroYak_CAF1 9625 118 - 1
GCGCAACUUUUGCUAACUGUGCGAAAGUU--UUUUAUGGCGCCGCGGACAAGUGGUCAGCGAUUUAAUUUUAAUUGUAUUUAGAUAAGAUUUAAUGGUGUUUGUUCUAAAGCAGAGCAAA
(((((((((((((.......)))))))))--.......))))(((.(((.....))).)))(((.(((((((.(((....))).))))))).)))....((((((((.....)))))))) ( -29.51)
>consensus
GCGCAACUUUUGCCAACUGUGCGAAAGUU_UUUUUAUGGCGCCGCGGACAAGUGGUCAGCGAUUUAAUUUUAAUUGUAUUUAGAUAAGAUUUAAUGGCGUUUGUUCUGGAGCAGAGCGCA
((((((((((((((....).)))))))))..(((((..(((((((......)))))..((.(((.(((((((.(((....))).))))))).))).))....))..)))))....)))). (-27.26 = -27.70 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	4,025,144 – 4,025,264
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.17
Mean single sequence MFE	-27.19
Consensus MFE	-24.72
Energy contribution	-24.64
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-1.22
Structure conservation index	0.91
SVM decision value	0.25
SVM RNA-class probability	0.653823
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4025144 120 + 20766785
AGUGUCGUAAAAAAGUCGUAAAAGUCGGUGGGGAAAUGCGAAAAAAUAAUUGCAUAAUUAGCAGCACUUGGCUAACAAGUUGUGACAGCAGAAACCACACCACGACCCGAAUUCGCAACU
.(.(((((......(.(......).)((((((....(((...........(((.......)))(((((((.....)))).)))....)))....)).))))))))).)............ ( -27.30)
>DroSec_CAF1 7947 120 + 1
AGUGUCGUAAAAAAGUCGUAAAAGUCGGUGGGGAAAGGCGAAAAAAUAAUUGCAUAAUUAGCAGCACUUGGCUAACAAGUUGUGACAGCAGAAACCACACCACGACCCGAAUCCGCAACU
.(.(((((......(.(......).)((((((.....((...........(((.......)))(((((((.....)))).)))....)).....)).))))))))).)............ ( -25.70)
>DroSim_CAF1 9997 120 + 1
AGUGUCGUAAAAAAGUCGUAAAAGUCGGUGGGGAAAUGCGAAAAAAUAAUUGCAUAAUUAGCAGCACUUGGCUAACAAGUUGUGACAGCAGAAACCACACCACGACCCGAAUUCGCAACU
.(.(((((......(.(......).)((((((....(((...........(((.......)))(((((((.....)))).)))....)))....)).))))))))).)............ ( -27.30)
>DroEre_CAF1 7191 120 + 1
AAUGUCGUAAAAAAGUUGUAAAAGUCGGUGGGGAAAUGCGAAAAAAUAAUUGCAUAAUUAGCAGCACUUGGCUAACAAGUUGCGACAGCAGAAACCACACCACGACCCCAAUUCGCAGCU
.............((((((....((.((((((....(((...........(((.......)))(((((((.....)))).)))....)))....)).))))))((.......)))))))) ( -28.30)
>DroYak_CAF1 9743 120 + 1
AGUGUCGUAAAAAAGUCGUAAAAGUCUGUGGGGAAAUGCGAAAAAAUAAUUGCAUAAUUAGCAGCACUUGGCUAACAAGUUGUGACAGCAGUAACCACAUCACGACCCCAAUUCGCCACU
((((.((.......(((((.......(((((....((((((........)))))).....((.(((((((.....)))).)))....)).....)))))..))))).......)).)))) ( -27.34)
>consensus
AGUGUCGUAAAAAAGUCGUAAAAGUCGGUGGGGAAAUGCGAAAAAAUAAUUGCAUAAUUAGCAGCACUUGGCUAACAAGUUGUGACAGCAGAAACCACACCACGACCCGAAUUCGCAACU
...(((((......(.(......).)((((((....(((...........(((.......)))(((((((.....)))).)))....)))....)).))))))))).............. (-24.72 = -24.64 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:29 2006