Locus 4834

Sequence ID	2R_DroMel_CAF1
Location	15,878,568 – 15,878,710
Length	142
Max. P	0.998511

overview

Window 6

Location	15,878,568 – 15,878,676
Length	108
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	94.38
Mean single sequence MFE	-26.68
Consensus MFE	-26.18
Energy contribution	-26.38
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.98
SVM decision value	3.13
SVM RNA-class probability	0.998511
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15878568 108 + 20766785
UACA------CAUGCUCCUACGAACAUCCGACUGCCGUUUGUCGCUGCGUAUUGGUACGUGCCGAAUGGCAACUGGAAAACUUUUUUAAUUUAAAAAAAUUCUGUGUUCUUUCG
....------...........(((((((((..(((((((((..((.(((((....))))))))))))))))..))))....(((((((...)))))))......)))))..... ( -26.80)
>DroSec_CAF1 15731 108 + 1
UACA------CAUACUCCUACGAACAUCCGACUGCCGUUUGUCGCUGCGUAUUGGUACGUGCCGAAUGGCAACUGGAAAACUUUUUUAAUUUAAAAAAAUUCUGUGUUCUUUCG
....------...........(((((((((..(((((((((..((.(((((....))))))))))))))))..))))....(((((((...)))))))......)))))..... ( -26.80)
>DroSim_CAF1 13154 108 + 1
UACA------CAUACUCCUACGAACAUCCGACUGCCGUUUGUCGCUGCGUAUUGGUACGUGCCGAAUGGCAACUGGAAAACUUUUUUAAUUUAAAAAAAUUCUGUGUUCUUUCG
....------...........(((((((((..(((((((((..((.(((((....))))))))))))))))..))))....(((((((...)))))))......)))))..... ( -26.80)
>DroEre_CAF1 13456 106 + 1
UACA------CAUGCCCCUACGAACAUCCGACUGCCGUUUGUCGCUGCGUAUUGGUACGUGCCGAAUGGCAACUGGAAAACUUUUUUAAUUUAAA-AAACUCUGUGUUCU-UCG
....------...........(((((((((..(((((((((..((.(((((....))))))))))))))))..))))....(((((((...))))-))).....))))).-... ( -26.50)
>DroYak_CAF1 15985 113 + 1
UACACACACACAUACCCCUACGAACAUCCGAAUGCCGUUUGUCGCUGCGUAUUGCUACGUGCCGAAUGGCAACUGGAAAACUUUUUUAAUUUAAAAAAAUUCUAUGUUCU-UCG
.....................(((((((((..(((((((((..((.(((((....))))))))))))))))..))))....(((((((...)))))))......))))).-... ( -26.50)
>consensus
UACA______CAUACUCCUACGAACAUCCGACUGCCGUUUGUCGCUGCGUAUUGGUACGUGCCGAAUGGCAACUGGAAAACUUUUUUAAUUUAAAAAAAUUCUGUGUUCUUUCG
.....................(((((((((..(((((((((..((.(((((....))))))))))))))))..))))....(((((((...)))))))......)))))..... (-26.18 = -26.38 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	15,878,602 – 15,878,710
Length	108
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	94.66
Mean single sequence MFE	-29.66
Consensus MFE	-25.52
Energy contribution	-25.56
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.85
Structure conservation index	0.86
SVM decision value	1.71
SVM RNA-class probability	0.973256
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15878602 108 - 20766785
UAGUGUCGUCCUUCGUCUUGGGU--UGGACUAGCUGCGAAAGAACACAGAAUUUUUUUAAAUUAAAAAAGUUUUCCAGUUGCCAUUCGGCACGUACCAAUACGCAGCGAC
....(((((((.((......)).--.))))..((((((....(((..((((((((((((...))))))))))))...)))(((....)))...........))))))))) ( -28.80)
>DroSec_CAF1 15765 108 - 1
UAGUGCCGUCCUUCGUCUUGGUU--UGGACUAGCUGCGAAAGAACACAGAAUUUUUUUAAAUUAAAAAAGUUUUCCAGUUGCCAUUCGGCACGUACCAAUACGCAGCGAC
((((.(((.((........))..--)))))))((((((....(((..((((((((((((...))))))))))))...)))(((....)))...........))))))... ( -28.60)
>DroSim_CAF1 13188 108 - 1
UAGUGCCGUCCUUCGUCUUGGUU--UGGACUAGCUGCGAAAGAACACAGAAUUUUUUUAAAUUAAAAAAGUUUUCCAGUUGCCAUUCGGCACGUACCAAUACGCAGCGAC
((((.(((.((........))..--)))))))((((((....(((..((((((((((((...))))))))))))...)))(((....)))...........))))))... ( -28.60)
>DroEre_CAF1 13490 106 - 1
CAGUCCCGUCCUUCGUCUUGGGU--UGGACUAGCUGCGA-AGAACACAGAGUUU-UUUAAAUUAAAAAAGUUUUCCAGUUGCCAUUCGGCACGUACCAAUACGCAGCGAC
.(((((..(((........))).--.))))).(((((((-(((((.....))))-))....................((.(((....))))).........))))))... ( -30.10)
>DroYak_CAF1 16025 109 - 1
UUGUCCCGUCCUUCGUCUUGGGUUUUGGACUCGCUGCGA-AGAACAUAGAAUUUUUUUAAAUUAAAAAAGUUUUCCAGUUGCCAUUCGGCACGUAGCAAUACGCAGCGAC
..((((...(((.......)))....))))(((((((..-..(((..((((((((((((...))))))))))))...)))(((....)))..(((....)))))))))). ( -32.20)
>consensus
UAGUGCCGUCCUUCGUCUUGGGU__UGGACUAGCUGCGAAAGAACACAGAAUUUUUUUAAAUUAAAAAAGUUUUCCAGUUGCCAUUCGGCACGUACCAAUACGCAGCGAC
.......(((....((((........))))..((((((....(((..((((((((((((...))))))))))))...)))(((....)))...........))))))))) (-25.52 = -25.56 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:24 2006