Locus 2408

Sequence ID	3R_DroMel_CAF1
Location	6,756,253 – 6,756,402
Length	149
Max. P	0.991379

overview

Window 9

Location	6,756,253 – 6,756,364
Length	111
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-34.67
Consensus MFE	-34.75
Energy contribution	-34.12
Covariance contribution	-0.62
Combinations/Pair	1.10
Mean z-score	-1.69
Structure conservation index	1.00
SVM decision value	1.02
SVM RNA-class probability	0.902236
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756253 111 + 27905053
ACAAUUUCUGCCGAUGUCGCCUCAGAUGUUUAUGUUGUUGUUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGGUG
(((((((.((((((((((......)))))).............(..(((((....)))))..)..(((((......)))))..)))).)))))))(((.((....)).))) ( -34.90)
>DroSec_CAF1 20426 111 + 1
ACAAUUUCUGCCGAUGUCGCCUCAGAUGUUUAUGUUGUUGUUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGAUG
.((((((.((((((((((......)))))).............(..(((((....)))))..)..(((((......)))))..)))).))))))((((.......)))).. ( -34.90)
>DroSim_CAF1 24806 111 + 1
ACAAUUUCUGCCGAUGUCGCCUCAGAUGUUUAUGUUGUUGUUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGAUG
.((((((.((((((((((......)))))).............(..(((((....)))))..)..(((((......)))))..)))).))))))((((.......)))).. ( -34.90)
>DroEre_CAF1 4864 103 + 1
ACAAUUUCUGCCGAUGUCGCCUCAGAUGUUUGU--------UGCUGCUUCUGUAAGGAAGUGGGCGGCACUUUUAUGUGCCAAGGCGAAAGUUGUCGCAGCUUUAGUGGUG
.........(((((((((......)))))).((--------(((.((((((....)))))).((((((((......)))))..(((....)))))))))))......))). ( -34.00)
>consensus
ACAAUUUCUGCCGAUGUCGCCUCAGAUGUUUAUGUUGUUGUUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGAUG
.((((((.((((((((((......)))))).............(..(((((....)))))..)..(((((......)))))..)))).))))))((((.......)))).. (-34.75 = -34.12 +  -0.62)

alignment

secondary structure

dotplot

Window 0

Location	6,756,253 – 6,756,364
Length	111
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-27.63
Consensus MFE	-26.94
Energy contribution	-26.75
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-2.46
Structure conservation index	0.98
SVM decision value	2.26
SVM RNA-class probability	0.991379
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756253 111 - 27905053
CACCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAACAACAACAUAAACAUCUGAGGCGACAUCGGCAGAAAUUGU
................((((.(((((((..(((((......)))))(((..(((((....)))))(((..................))).)))......))))))).)))) ( -27.57)
>DroSec_CAF1 20426 111 - 1
CAUCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAACAACAACAUAAACAUCUGAGGCGACAUCGGCAGAAAUUGU
................((((.(((((((..(((((......)))))(((..(((((....)))))(((..................))).)))......))))))).)))) ( -27.57)
>DroSim_CAF1 24806 111 - 1
CAUCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAACAACAACAUAAACAUCUGAGGCGACAUCGGCAGAAAUUGU
................((((.(((((((..(((((......)))))(((..(((((....)))))(((..................))).)))......))))))).)))) ( -27.57)
>DroEre_CAF1 4864 103 - 1
CACCACUAAAGCUGCGACAACUUUCGCCUUGGCACAUAAAAGUGCCGCCCACUUCCUUACAGAAGCAGCA--------ACAAACAUCUGAGGCGACAUCGGCAGAAAUUGU
...........((((((......((((((((((((......)))))((...((((......))))..)).--------..........)))))))..)).))))....... ( -27.80)
>consensus
CACCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAACAACAACAUAAACAUCUGAGGCGACAUCGGCAGAAAUUGU
...........((((((......((((((((((((......)))))((...((((......))))..))...................)))))))..)).))))....... (-26.94 = -26.75 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	6,756,293 – 6,756,402
Length	109
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	88.29
Mean single sequence MFE	-34.88
Consensus MFE	-29.90
Energy contribution	-29.78
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.86
SVM decision value	1.01
SVM RNA-class probability	0.900071
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756293 109 + 27905053
UUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGGUGCCACCCAACACCACCCACCACCA--ACCCGACUUGCACCG
.(((.((((((....))))))(((.(((((......)))))..((..(((((((...))))))).((((((........))))))...))....--.))).....)))... ( -36.50)
>DroSec_CAF1 20466 111 + 1
UUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGAUGCGACCCAACACCACCCACCACAACCACCCGACUUGCACCG
.(((.((((((....))))))(((.(((((......)))))..((.....(((((((((.(......).))))))..))).....))..........))).....)))... ( -33.20)
>DroSim_CAF1 24846 111 + 1
UUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGAUGCCACCAAACACCACCCACCAUUACCACCCGACUUGCACCG
.(((.((((((....))))))(((.(((((......)))))..(((((((((((...))))))).....))))...........)))..................)))... ( -31.80)
>DroEre_CAF1 4897 97 + 1
-UGCUGCUUCUGUAAGGAAGUGGGCGGCACUUUUAUGUGCCAAGGCGAAAGUUGUCGCAGCUUUAGUGGUGCCACCCAGC----------A---CCACCCCAUUUGCACCG
-(((.((((((....))))))(((.(((((......)))))...((((......)))).......(((((((......))----------)---)))))))....)))... ( -38.00)
>consensus
UUGCUGCUUCUGUAAAGAAGUGGGCGGCACUUUUAUGUGCCAAGGCAAAAGUUGUCGCAGCUUUAGUGAUGCCACCCAACACCACCCACCAC_ACCACCCGACUUGCACCG
.(((.((((((....))))))(((.(((((......)))))..(((((((((((...))))))).....))))........................))).....)))... (-29.90 = -29.78 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	6,756,293 – 6,756,402
Length	109
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	88.29
Mean single sequence MFE	-39.73
Consensus MFE	-29.73
Energy contribution	-30.97
Covariance contribution	1.25
Combinations/Pair	1.10
Mean z-score	-2.00
Structure conservation index	0.75
SVM decision value	0.66
SVM RNA-class probability	0.815227
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756293 109 - 27905053
CGGUGCAAGUCGGGU--UGGUGGUGGGUGGUGUUGGGUGGCACCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAA
.((((.((((...((--(.(..((.(((((((((....)))))))))...))..)))).)))).))))..(((((......)))))((...(((((....)))))..)).. ( -40.30)
>DroSec_CAF1 20466 111 - 1
CGGUGCAAGUCGGGUGGUUGUGGUGGGUGGUGUUGGGUCGCAUCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAA
...(((.....((((.((((..((.((((((((......))))))))...))..))))............(((((......))))))))).(((((....)))))..))). ( -42.20)
>DroSim_CAF1 24846 111 - 1
CGGUGCAAGUCGGGUGGUAAUGGUGGGUGGUGUUUGGUGGCAUCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAA
...(((.....(((((((((.((((.(..((.(((((((....)))))))))..)..).))).)))))..(((((......))))))))).(((((....)))))..))). ( -39.50)
>DroEre_CAF1 4897 97 - 1
CGGUGCAAAUGGGGUGG---U----------GCUGGGUGGCACCACUAAAGCUGCGACAACUUUCGCCUUGGCACAUAAAAGUGCCGCCCACUUCCUUACAGAAGCAGCA-
.(.(((...((((((((---(----------(((....)))))))).......((((......))))...(((((......))))).)))).(((......)))))).).- ( -36.90)
>consensus
CGGUGCAAGUCGGGUGGU_GUGGUGGGUGGUGUUGGGUGGCACCACUAAAGCUGCGACAACUUUUGCCUUGGCACAUAAAAGUGCCGCCCACUUCUUUACAGAAGCAGCAA
.(.(((.....((((..........(((((((((....)))))))))......((((......))))...(((((......)))))))))..(((......)))))).).. (-29.73 = -30.97 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:01 2006