Locus 1887

Sequence ID	3R_DroMel_CAF1
Location	5,407,592 – 5,407,779
Length	187
Max. P	0.915062

overview

Window 6

Location	5,407,592 – 5,407,700
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.25
Mean single sequence MFE	-39.59
Consensus MFE	-25.80
Energy contribution	-25.80
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-2.95
Structure conservation index	0.65
SVM decision value	0.05
SVM RNA-class probability	0.558992
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5407592 108 - 27905053
ACGUUUCCAUGACGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCA------AUGGCG-AUGACAACGAUGGCG---AUAUGUGGCCAAUGCAACUGCAACUGCAA
............((((-((((((.......))))-))))))....(((.(((((((((..------.((((.-((.....((....))---....)).)))))))).)))))....))). ( -38.80)
>DroSec_CAF1 11528 111 - 1
ACGUUUCCAUGGCGUUAGGCCGCAAACAAAGUGGUCCAGCGAAAAUGCGGCAGUGCAUCA------ACGGCGAAUGACAACGUUGGCA---AUAUGCGGCCAUGCCAACUGCAACUGCAA
..(((..(((((((((.((((((.......)))))).))).........(((.(((..((------(((...........))))))))---...))).))))))..)))(((....))). ( -36.10)
>DroSim_CAF1 6480 108 - 1
ACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCA------ACGGCG-AUGACAACGUUGGCG---AUAUGCGGCCAAUGCAACUGCAACUGCAA
.(((........((((-((((((.......))))-)))))).....)))((((((((...------.((.((-(((....))))).))---...((((.....))))..))).))))).. ( -41.42)
>DroEre_CAF1 10775 114 - 1
ACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCAAAAUCAAAAGCG-GUGACAACGAUGGCA---AUAUGUGGCUAAUGCAACUGCAACUGCAA
.(((........((((-((((((.......))))-)))))).....)))(((((((((.............(-....).....((((.---.......)))))))).)))))........ ( -37.02)
>DroYak_CAF1 6591 111 - 1
ACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCA------AAAGCG-GCGACAACGUUGGCAACAAUAUGUGGCCAAUGCAACUGCAACUGCAA
.(((........((((-((((((.......))))-)))))).....)))(((((((....------...))(-((.(((..((((....)))).))).)))..(((....)))))))).. ( -44.62)
>consensus
ACGUUUCCAUGGCGUU_GGCCGCAAACAAAGUGG_CCAGCGAAAAUGCGGCAGUGCAUCA______AAGGCG_AUGACAACGUUGGCA___AUAUGUGGCCAAUGCAACUGCAACUGCAA
.(((........((((.((((((.......)))).)))))).....)))((((((((...........((((........))))(((...........)))........))).))))).. (-25.80 = -25.80 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	5,407,629 – 5,407,739
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.71
Mean single sequence MFE	-41.58
Consensus MFE	-31.79
Energy contribution	-31.73
Covariance contribution	-0.05
Combinations/Pair	1.10
Mean z-score	-3.65
Structure conservation index	0.76
SVM decision value	1.10
SVM RNA-class probability	0.915062
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5407629 110 - 27905053
CGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGACGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCA------AUGGCG-AUGACAA
.....(((((......-(((((((((((((....))))....))))))))).((((-((((((.......))))-))))))....)))))..((.((((.------.....)-))))).. ( -44.00)
>DroSec_CAF1 11565 114 - 1
CGAAAUCGCACACGAACCAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUUAGGCCGCAAACAAAGUGGUCCAGCGAAAAUGCGGCAGUGCAUCA------ACGGCGAAUGACAA
.....((((.......((((((((((((((....))))....))))))))))((((.((((((.......)))))).))))...(((((....)))))..------...))))....... ( -38.70)
>DroSim_CAF1 6517 110 - 1
CGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCA------ACGGCG-AUGACAA
.....(((((......-(((((((((((((....))))....))))))))).((((-((((((.......))))-))))))....)))))..((.((((.------.....)-))))).. ( -43.90)
>DroEre_CAF1 10812 116 - 1
CGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCAAAAUCAAAAGCG-GUGACAA
.(..(((((.......-(((((((((((((....))))....))))))))).((((-((((((.......))))-))))))...(((((....)))))...........)))-))..).. ( -43.20)
>DroYak_CAF1 6631 110 - 1
CGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGCGAAAAUGCGGCAGUGCAUCA------AAAGCG-GCGACAA
.....((((.......-(((((((((((((....))))....)))))))))(((((-((((((.......))))-)))))....(((((....)))))..------...)).-))))... ( -43.00)
>DroAna_CAF1 6352 99 - 1
CGAAAUCGCAGACAAA-CAUGGAAAUCGCACAGGUGCGACACGUUUCCAUGGUGGC-GGCCACAAGU-CAGUGG-CCAGCGAAACGGCAAUAAUGCAUUA------AUA-----------
((...((((.......-(((((((((((((....)))))....)))))))).....-((((((....-..))))-)).))))..))(((....)))....------...----------- ( -36.70)
>consensus
CGAAAUCGCACACGAA_CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU_GGCCGCAAACAAAGUGG_CCAGCGAAAAUGCGGCAGUGCAUCA______AAAGCG_AUGACAA
.....((((..(((...(((((((((((((....))))....))))))))).)))..((((((.......)))).)).))))..(((((....)))))...................... (-31.79 = -31.73 +  -0.05)

alignment

secondary structure

dotplot

Window 8

Location	5,407,662 – 5,407,779
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.28
Mean single sequence MFE	-45.50
Consensus MFE	-35.73
Energy contribution	-35.82
Covariance contribution	0.09
Combinations/Pair	1.14
Mean z-score	-2.71
Structure conservation index	0.79
SVM decision value	0.36
SVM RNA-class probability	0.703800
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5407662 117 - 27905053
UGAUGGAGGUCCAGGAAGUGGCUGUUAUUGCUGCCAUUUUCGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGACGUU-GGCCGCAAACAAAGUGG-CCAGC
...(((....)))(((((((((.((....)).)))))))))....(((....))).-(((((((((((((....))))....)))))))))..(((-((((((.......))))-))))) ( -47.60)
>DroSec_CAF1 11599 120 - 1
UGAUGGAGGUCCAGGAAGUGGCUGUUGUUGCUGCCAUUUUCGAAAUCGCACACGAACCAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUUAGGCCGCAAACAAAGUGGUCCAGC
...(((....)))(((((((((.((....)).)))))))))....(((....))).((((((((((((((....))))....)))))))))).(((.((((((.......)))))).))) ( -44.30)
>DroSim_CAF1 6550 117 - 1
UGAUGGAGGUCCAGGAAGUGGCUGUUGUUGCUGCCAUUUUCGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGC
...(((....)))(((((((((.((....)).)))))))))....(((....))).-(((((((((((((....))))....)))))))))..(((-((((((.......))))-))))) ( -47.80)
>DroEre_CAF1 10851 117 - 1
UGAUGGAGGUCCAGGAAGUGGCUGUUGCUUACGCCACUUUCGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGC
...(((....)))(((((((((.((.....)))))))))))....(((....))).-(((((((((((((....))))....)))))))))..(((-((((((.......))))-))))) ( -48.80)
>DroYak_CAF1 6664 117 - 1
UGAUGGAGGUCCAGGAAGUGGCUGUUGUUUACGCCACUCUCGAAAUCGCACACGAA-CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU-GGCCGCAAACAAAGUGG-CCAGC
...(((....)))(..((((((.((.....))))))))..)....(((....))).-(((((((((((((....))))....)))))))))..(((-((((((.......))))-))))) ( -46.20)
>DroAna_CAF1 6375 110 - 1
UGAUAGAGAUCCAAGAAAU------UGUUGCUGCCAUUUUCGAAAUCGCAGACAAA-CAUGGAAAUCGCACAGGUGCGACACGUUUCCAUGGUGGC-GGCCACAAGU-CAGUGG-CCAGC
...........(((....)------))..(((((((((((((....)).)))....-(((((((((((((....)))))....)))))))))))))-((((((....-..))))-))))) ( -38.30)
>consensus
UGAUGGAGGUCCAGGAAGUGGCUGUUGUUGCUGCCAUUUUCGAAAUCGCACACGAA_CAUGGAAAUCGCACAGGUGCGGCACGUUUCCAUGGCGUU_GGCCGCAAACAAAGUGG_CCAGC
.......(((...(((((((((..........)))))))))...)))((..(((...(((((((((((((....))))....))))))))).)))..((((((.......)))).)).)) (-35.73 = -35.82 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:56 2006