Locus 3955

Sequence ID	X_DroMel_CAF1
Location	10,514,682 – 10,514,805
Length	123
Max. P	0.999968

overview

Window 3

Location	10,514,682 – 10,514,775
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	96.88
Mean single sequence MFE	-34.80
Consensus MFE	-31.84
Energy contribution	-31.88
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.52
Structure conservation index	0.91
SVM decision value	3.61
SVM RNA-class probability	0.999441
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10514682 93 + 22224390
GAAAGGCUAUUGAAAGAAGAGUCCUUGGAAGGAGAGGGUGGGGUCCUCCAUGCUGGAGGAUGCCGGAUUGGCCAACACUCGGCCAGAUAUCUC
..((((((.((....))..)).)))).....((((...(((.(((((((.....))))))).)))..((((((.......))))))...)))) ( -33.00)
>DroSec_CAF1 45983 93 + 1
GAAAGGCUAUUGAAAGAAGAGUCCUUGGAAGGAGAGGGAGGGGUCCUCCAUGCUGGAGGACGCCAGAUUGGCCAACACUCGGCCAGAUAUCUC
..((((((.((....))..)).)))).....((((....((.(((((((.....))))))).))...((((((.......))))))...)))) ( -34.50)
>DroSim_CAF1 49320 93 + 1
GAAAGGCUAUUGAAAGAAGAGUCCUUGGAAGGAGAGGGUGGGGUCCUCCAUGCUGGAGGACGCCGGAUUGGCCAACACUCGGCCAGAUAUCUC
..((((((.((....))..)).)))).....((((...(((.(((((((.....))))))).)))..((((((.......))))))...)))) ( -34.50)
>DroEre_CAF1 46662 93 + 1
GAAAGGCUAUUGAAAGAAGAGUCCUUGGAAGGAGAGGGUGGGGUCCUCCAUGCUGGAGGACGACGGUUUGGCCAACACUUGGCCAGAUAUCUC
..((((((.((....))..)).)))).....((((...((..(((((((.....)))))))..))(((((((((.....))))))))).)))) ( -34.30)
>DroYak_CAF1 47912 93 + 1
GAAAGGCUAUUGAAAGAAGAGUCCUUGGAAGGAGAGGGCGGGGUCCUCCAUGCUGGAGGACGCCGGAUUGGCCAACACUUGGCCAGAUAUCUC
..((((((.((....))..)).)))).....((((...(((.(((((((.....))))))).)))..(((((((.....)))))))...)))) ( -37.70)
>consensus
GAAAGGCUAUUGAAAGAAGAGUCCUUGGAAGGAGAGGGUGGGGUCCUCCAUGCUGGAGGACGCCGGAUUGGCCAACACUCGGCCAGAUAUCUC
..((((((.((.....)).)).)))).....((((....((.(((((((.....))))))).))...((((((.......))))))...)))) (-31.84 = -31.88 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	10,514,682 – 10,514,775
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	96.88
Mean single sequence MFE	-29.98
Consensus MFE	-29.26
Energy contribution	-29.42
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.98
Structure conservation index	0.98
SVM decision value	5.00
SVM RNA-class probability	0.999968
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10514682 93 - 22224390
GAGAUAUCUGGCCGAGUGUUGGCCAAUCCGGCAUCCUCCAGCAUGGAGGACCCCACCCUCUCCUUCCAAGGACUCUUCUUUCAAUAGCCUUUC
(((.....(((((((...)))))))....((..((((((.....))))))..))...)))((((....))))..................... ( -27.50)
>DroSec_CAF1 45983 93 - 1
GAGAUAUCUGGCCGAGUGUUGGCCAAUCUGGCGUCCUCCAGCAUGGAGGACCCCUCCCUCUCCUUCCAAGGACUCUUCUUUCAAUAGCCUUUC
.((((...(((((((...)))))))))))((((((((((.....))))))).........((((....))))..............))).... ( -31.40)
>DroSim_CAF1 49320 93 - 1
GAGAUAUCUGGCCGAGUGUUGGCCAAUCCGGCGUCCUCCAGCAUGGAGGACCCCACCCUCUCCUUCCAAGGACUCUUCUUUCAAUAGCCUUUC
(((.....(((((((...)))))))....((.(((((((.....))))))).))...)))((((....))))..................... ( -30.80)
>DroEre_CAF1 46662 93 - 1
GAGAUAUCUGGCCAAGUGUUGGCCAAACCGUCGUCCUCCAGCAUGGAGGACCCCACCCUCUCCUUCCAAGGACUCUUCUUUCAAUAGCCUUUC
(((.....((((((.....))))))....(..(((((((.....)))))))..)...)))((((....))))..................... ( -28.00)
>DroYak_CAF1 47912 93 - 1
GAGAUAUCUGGCCAAGUGUUGGCCAAUCCGGCGUCCUCCAGCAUGGAGGACCCCGCCCUCUCCUUCCAAGGACUCUUCUUUCAAUAGCCUUUC
(((.....((((((.....))))))...(((.(((((((.....))))))).)))..)))((((....))))..................... ( -32.20)
>consensus
GAGAUAUCUGGCCGAGUGUUGGCCAAUCCGGCGUCCUCCAGCAUGGAGGACCCCACCCUCUCCUUCCAAGGACUCUUCUUUCAAUAGCCUUUC
(((.....(((((((...)))))))....((.(((((((.....))))))).))...)))((((....))))..................... (-29.26 = -29.42 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	10,514,715 – 10,514,805
Length	90
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	89.81
Mean single sequence MFE	-40.56
Consensus MFE	-34.34
Energy contribution	-34.58
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.47
Structure conservation index	0.85
SVM decision value	2.73
SVM RNA-class probability	0.996675
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10514715 90 + 22224390
GAGGGUGGGGUCCUCCAUGCUGGAGGAUGCCGGAUUGGCCAACACUCGGCCAGAUAUCUCCAGCAGGCUGCACUGCAUCCAAGCAUCAGU------
..((((((.(((((((.....))))))).))(((((((((.......)))))).....))).((((......))))))))..........------ ( -38.20)
>DroSec_CAF1 46016 90 + 1
GAGGGAGGGGUCCUCCAUGCUGGAGGACGCCAGAUUGGCCAACACUCGGCCAGAUAUCUCCAGCAGGCUGCACUGCAUCGAAGCGUCAUU------
((.(((((((((((((.....))))))).))...((((((.......))))))....)))).((((......)))).))...........------ ( -38.20)
>DroSim_CAF1 49353 90 + 1
GAGGGUGGGGUCCUCCAUGCUGGAGGACGCCGGAUUGGCCAACACUCGGCCAGAUAUCUCCAGCAGGCUGCACUGCAUCGGAGCAUCAUU------
.....(((.(((((((.....))))))).)))...(((((.......)))))(((..((((.((((......))))...)))).)))...------ ( -39.10)
>DroEre_CAF1 46695 96 + 1
GAGGGUGGGGUCCUCCAUGCUGGAGGACGACGGUUUGGCCAACACUUGGCCAGAUAUCUCCAGCAGGCUGCACUGCAUCCGAGCAUCAGUGUGGAA
((((.((..(((((((.....)))))))..))(((((((((.....))))))))).))))..((((......)))).((((.((....)).)))). ( -41.20)
>DroYak_CAF1 47945 96 + 1
GAGGGCGGGGUCCUCCAUGCUGGAGGACGCCGGAUUGGCCAACACUUGGCCAGAUAUCUCCAGCACGCUGCACUGCAUCCGAGCACCAGUGUGGCA
((((.(((.(((((((.....))))))).)))..(((((((.....)))))))...))))......((..(((((...........)))))..)). ( -46.10)
>consensus
GAGGGUGGGGUCCUCCAUGCUGGAGGACGCCGGAUUGGCCAACACUCGGCCAGAUAUCUCCAGCAGGCUGCACUGCAUCCGAGCAUCAGU______
((((..((.(((((((.....))))))).))...((((((.......))))))...))))..((((......)))).................... (-34.34 = -34.58 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	10,514,715 – 10,514,805
Length	90
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	89.81
Mean single sequence MFE	-36.58
Consensus MFE	-32.08
Energy contribution	-32.24
Covariance contribution	0.16
Combinations/Pair	1.11
Mean z-score	-1.74
Structure conservation index	0.88
SVM decision value	1.43
SVM RNA-class probability	0.952823
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10514715 90 - 22224390
------ACUGAUGCUUGGAUGCAGUGCAGCCUGCUGGAGAUAUCUGGCCGAGUGUUGGCCAAUCCGGCAUCCUCCAGCAUGGAGGACCCCACCCUC
------.(((.(((......)))...)))..(((((((......(((((((...))))))).)))))))((((((.....)))))).......... ( -34.50)
>DroSec_CAF1 46016 90 - 1
------AAUGACGCUUCGAUGCAGUGCAGCCUGCUGGAGAUAUCUGGCCGAGUGUUGGCCAAUCUGGCGUCCUCCAGCAUGGAGGACCCCUCCCUC
------..............((((......)))).((((.....(((((((...)))))))....((.(((((((.....)))))))))))))... ( -34.30)
>DroSim_CAF1 49353 90 - 1
------AAUGAUGCUCCGAUGCAGUGCAGCCUGCUGGAGAUAUCUGGCCGAGUGUUGGCCAAUCCGGCGUCCUCCAGCAUGGAGGACCCCACCCUC
------...(((((((((..((((......))))))))).))))(((((((...)))))))....((.(((((((.....))))))).))...... ( -39.20)
>DroEre_CAF1 46695 96 - 1
UUCCACACUGAUGCUCGGAUGCAGUGCAGCCUGCUGGAGAUAUCUGGCCAAGUGUUGGCCAAACCGUCGUCCUCCAGCAUGGAGGACCCCACCCUC
.(((((((((.(((......)))...)))..)).))))(((...((((((.....))))))....)))(((((((.....)))))))......... ( -34.10)
>DroYak_CAF1 47945 96 - 1
UGCCACACUGGUGCUCGGAUGCAGUGCAGCGUGCUGGAGAUAUCUGGCCAAGUGUUGGCCAAUCCGGCGUCCUCCAGCAUGGAGGACCCCGCCCUC
.((((((((.(.((.(((((((((..(...)..)))....))))))))).)))).)))).....(((.(((((((.....))))))).)))..... ( -40.80)
>consensus
______ACUGAUGCUCGGAUGCAGUGCAGCCUGCUGGAGAUAUCUGGCCGAGUGUUGGCCAAUCCGGCGUCCUCCAGCAUGGAGGACCCCACCCUC
.........(((((((....((((......))))..))).))))(((((((...)))))))....((.(((((((.....))))))).))...... (-32.08 = -32.24 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:41 2006