Locus 10045

Sequence ID	3R_DroMel_CAF1
Location	26,914,632 – 26,914,766
Length	134
Max. P	0.939845

overview

Window 7

Location	26,914,632 – 26,914,729
Length	97
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	76.07
Mean single sequence MFE	-22.58
Consensus MFE	-11.79
Energy contribution	-12.40
Covariance contribution	0.61
Combinations/Pair	1.17
Mean z-score	-1.70
Structure conservation index	0.52
SVM decision value	0.08
SVM RNA-class probability	0.575004
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26914632 97 - 27905053
GCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC--------ACGAAAAAACACACACAUUACGGGGACCGCAGACAAAGG-AC
((..(((((((((....(((..........)))....))))))))).......(((--------.((.................)))))...)).........-.. ( -22.53)
>DroGri_CAF1 25376 84 - 1
UU------AGAGCCAUUAGCUAAUUAAG-UGCCC-AAUGUUUCUGGGCACCCACUC--------ACAAGGAAACU-----AGUGGAAAAACCGCAGACAAUAGCA-
..------..........((((.....(-(((((-(.......)))))))(((((.--------...((....))-----)))))...............)))).- ( -25.10)
>DroSec_CAF1 17416 97 - 1
GCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC--------ACGAAAAAACACACACAUUACGGGGACCGCAGACAAAGG-AC
((..(((((((((....(((..........)))....))))))))).......(((--------.((.................)))))...)).........-.. ( -22.53)
>DroSim_CAF1 16574 97 - 1
GCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC--------ACGAAAAAACACACACAUUACGGGGACCGCAGACAAAGG-AC
((..(((((((((....(((..........)))....))))))))).......(((--------.((.................)))))...)).........-.. ( -22.53)
>DroYak_CAF1 16311 105 - 1
GCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCGCCCUCGAAAAAACGAAAAAACACACACAUUACGGCAGCCGCAGACAAAGG-AC
((..(((((((((....(((..........)))....)))))))))...((((...(((......)))................))))....)).........-.. ( -23.01)
>DroAna_CAF1 22620 87 - 1
GUAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUG----CCACCC--------AC------ACCCUUAAAUUUUCGAAACCGCAGACAAAAG-AC
((.((((((((((....(((..........)))....)))))))))----).))..--------..------...(((...(((.((....)).)))...)))-.. ( -19.80)
>consensus
GCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC________ACGAAAAAACACACACAUUACGGGAACCGCAGACAAAGG_AC
....(((((((((....(((..........)))....)))))))))............................................................ (-11.79 = -12.40 +   0.61)

alignment

secondary structure

dotplot

Window 8

Location	26,914,670 – 26,914,766
Length	96
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	92.91
Mean single sequence MFE	-35.08
Consensus MFE	-31.38
Energy contribution	-31.27
Covariance contribution	-0.11
Combinations/Pair	1.08
Mean z-score	-1.43
Structure conservation index	0.89
SVM decision value	0.62
SVM RNA-class probability	0.801789
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26914670 96 + 27905053
CGU--------GGGUGGCUUCCAAGGCAACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUGCCUUGCGGCCUUGCAGGCACGAAAAAGGGCUUAGACUG
...--------.(((......((((((((((...(((..........)))...))))))))))..(((((.(((((.....))).))....)))))....))). ( -33.10)
>DroSec_CAF1 17454 96 + 1
CGU--------GGGUGGCUUCCAAGGCAACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUGCCUUGCGGCCUUGCAGGCACGAAAAAGGGCUUAGACUG
...--------.(((......((((((((((...(((..........)))...))))))))))..(((((.(((((.....))).))....)))))....))). ( -33.10)
>DroSim_CAF1 16612 96 + 1
CGU--------GGGUGGCUUCCAAGGCAACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUGCCUUGCGGCCUUGCAGGCACGAAAAAGGGCUUAGACUG
...--------.(((......((((((((((...(((..........)))...))))))))))..(((((.(((((.....))).))....)))))....))). ( -33.10)
>DroEre_CAF1 15711 96 + 1
CGU--------GGGUGGCUUCCAAGGCGACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUGCCUGGCGGCCUUGCAGGCACGAAAAAGGGCUUAGACUG
..(--------(((((((...((((((((((...(((..........)))...))))))))))..)))...(((((.....))).)).......)))))..... ( -32.60)
>DroYak_CAF1 16349 104 + 1
CGUUUUUUCGAGGGCGGCUUCCAAGGCAACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUGCCUUGCGGCCUUGCAGGCACGAAAAAGGGCUUAGACUG
(.((((((((((((((((....(((((((((...(((..........)))...)))))))))))))))))...(((.....))).)))))))).)......... ( -40.60)
>DroAna_CAF1 22653 91 + 1
-GU--------GGGUGG----CAAGGCAACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUACCAUACGGCCUUGCAGGCACGAAAAAGAGCUUAGACGG
-..--------.(((((----((((((((((...(((..........)))...)))))))))))))))...(((((.....))).))................. ( -38.00)
>consensus
CGU________GGGUGGCUUCCAAGGCAACUCGGAGCGUCUUAAUUAGCUAAUGGUUGCCUUGCUGCCUUGCGGCCUUGCAGGCACGAAAAAGGGCUUAGACUG
...........(((((((...((((((((((...(((..........)))...))))))))))..)))...(((((.....))).)).......))))...... (-31.38 = -31.27 +  -0.11)

alignment

secondary structure

dotplot

Window 9

Location	26,914,670 – 26,914,766
Length	96
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	92.91
Mean single sequence MFE	-30.39
Consensus MFE	-27.43
Energy contribution	-27.79
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.67
Structure conservation index	0.90
SVM decision value	1.30
SVM RNA-class probability	0.939845
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26914670 96 - 27905053
CAGUCUAAGCCCUUUUUCGUGCCUGCAAGGCCGCAAGGCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC--------ACG
..((((.(((.........(((((((...(((....))).)).))))).......))).....))))((((((((....))))).))).....--------... ( -31.09)
>DroSec_CAF1 17454 96 - 1
CAGUCUAAGCCCUUUUUCGUGCCUGCAAGGCCGCAAGGCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC--------ACG
..((((.(((.........(((((((...(((....))).)).))))).......))).....))))((((((((....))))).))).....--------... ( -31.09)
>DroSim_CAF1 16612 96 - 1
CAGUCUAAGCCCUUUUUCGUGCCUGCAAGGCCGCAAGGCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC--------ACG
..((((.(((.........(((((((...(((....))).)).))))).......))).....))))((((((((....))))).))).....--------... ( -31.09)
>DroEre_CAF1 15711 96 - 1
CAGUCUAAGCCCUUUUUCGUGCCUGCAAGGCCGCCAGGCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUCGCCUUGGAAGCCACCC--------ACG
..((((.(((.........(((((((...(((....))).)).))))).......))).....))))((((((((....))))).))).....--------... ( -28.09)
>DroYak_CAF1 16349 104 - 1
CAGUCUAAGCCCUUUUUCGUGCCUGCAAGGCCGCAAGGCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCGCCCUCGAAAAAACG
............(((((((.((..((...(((....)))..(((((((((....(((..........)))....)))))))))...)).))...)))))))... ( -32.60)
>DroAna_CAF1 22653 91 - 1
CCGUCUAAGCUCUUUUUCGUGCCUGCAAGGCCGUAUGGUAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUG----CCACCC--------AC-
.................((.(((.....)))))...(((.((((((((((....(((..........)))....)))))))))----).))).--------..- ( -28.40)
>consensus
CAGUCUAAGCCCUUUUUCGUGCCUGCAAGGCCGCAAGGCAGCAAGGCAACCAUUAGCUAAUUAAGACGCUCCGAGUUGCCUUGGAAGCCACCC________ACG
..((((.(((.........(((((((...(((....))).)).))))).......))).....))))((((((((....))))).)))................ (-27.43 = -27.79 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:47:38 2006