Locus 7515

Sequence ID	X_DroMel_CAF1
Location	18,779,346 – 18,779,535
Length	189
Max. P	0.751182

overview

Window 0

Location	18,779,346 – 18,779,457
Length	111
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	80.59
Mean single sequence MFE	-31.80
Consensus MFE	-21.42
Energy contribution	-22.55
Covariance contribution	1.13
Combinations/Pair	1.13
Mean z-score	-1.59
Structure conservation index	0.67
SVM decision value	0.00
SVM RNA-class probability	0.533955
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779346 111 - 22224390
UUGUGUCUUAGCCUGGCCAAAAACUGGCAUGCCAAAAAGG----GGGAGAAAUCAGUGAAAGGCUUGACUCGGAAACGGGGACAUUCUCCAGACUUUAAGUCGCAAAGACCAGCA
(((.(((((.((...((((.....)))).......((((.----.((((((.(((((.....)).)))((((....))))....))))))...)))).....)).)))))))).. ( -33.30)
>DroSec_CAF1 25840 110 - 1
UUGUGUCUUAGCCUGGCCAAAAGCUGGCAUGCCAAAAUAG----G-GGGAAAUCAGUGAAAGGCUUGACGUGGAAACAGGGACAUUCUCCAGGCUUUAAGUCGCAAAUACCCGCA
(((((.((((((((((((....(((((..(.((.......----.-)).)..)))))....)))....(.((....)).).........))))))..))).)))))......... ( -33.60)
>DroEre_CAF1 24353 98 - 1
UUGUGUCUUUGCCUGGCCAAAAACUGGCAUACCCAAAUGGGCAGG-AGGAAAUCAGUGAAAGGCUUGAC----------------UCUUCAGGCUUUAAGUCGCAAAUCUAGGCA
...((((((..((((((((.....))))...(((....)))))))-..)).....(((((((((((((.----------------...)))))))))...)))).......)))) ( -30.90)
>DroYak_CAF1 24035 110 - 1
UUGUGUCUUGGCCUGGCCAAAAACUGGCAUACCAAAAUGG----G-GGGAAAUCAGUGAAAGGCUUGACUCGGAAACAGGCACACUCUCCAAGCUUUAAAUCGCAAAUCCAGGCA
..........(((((((((.....))))...((.....))----.-.........((((((((((((....(....)((.....))...))))))))...)))).....))))). ( -29.40)
>consensus
UUGUGUCUUAGCCUGGCCAAAAACUGGCAUACCAAAAUGG____G_GGGAAAUCAGUGAAAGGCUUGACUCGGAAACAGGGACAUUCUCCAGGCUUUAAGUCGCAAAUACAGGCA
(((((.(((((((((((((.....))))..................((((..(((((.....)).)))((((....)))).....))))))))))..))).)))))......... (-21.42 = -22.55 +   1.13)

alignment

secondary structure

dotplot

Window 1

Location	18,779,381 – 18,779,497
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.52
Mean single sequence MFE	-33.30
Consensus MFE	-23.87
Energy contribution	-24.56
Covariance contribution	0.69
Combinations/Pair	1.10
Mean z-score	-1.51
Structure conservation index	0.72
SVM decision value	0.06
SVM RNA-class probability	0.564424
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779381 116 - 22224390
AAGGGCUCCGCAGCCCCAACCCUGAAAUGAAAUACAGUCAUUGUGUCUUAGCCUGGCCAAAAACUGGCAUGCCAAAAAGG----GGGAGAAAUCAGUGAAAGGCUUGACUCGGAAACGGG
..(((((....)))))(((.(((..............((((((..((((..(((.((((.....)))).........)))----..))))...)))))).))).))).((((....)))) ( -35.06)
>DroSec_CAF1 25875 115 - 1
AAGGGCUCCGCAGCCCCAACCCUGAAAUGAAACACAGUCAUUGUGUCUUAGCCUGGCCAAAAGCUGGCAUGCCAAAAUAG----G-GGGAAAUCAGUGAAAGGCUUGACGUGGAAACAGG
..(((((....)))))....((((...(((.......)))(..((((..(((((.((((.....)))).(.((......)----)-.)............))))).))))..)...)))) ( -32.00)
>DroEre_CAF1 24383 108 - 1
AAGGGCUCCACAGCCCCAACCCUGAAAUGAAACACAGUCAUUGUGUCUUUGCCUGGCCAAAAACUGGCAUACCCAAAUGGGCAGG-AGGAAAUCAGUGAAAGGCUUGAC-----------
..(((((....)))))(((.(((..............((((((..(((...((((((((.....))))...(((....)))))))-.)))...)))))).))).)))..----------- ( -34.26)
>DroYak_CAF1 24070 115 - 1
AAGGGCUCCACAGCCCCAACCCUGAAAUGAAACACAGUCAUUGUGUCUUGGCCUGGCCAAAAACUGGCAUACCAAAAUGG----G-GGGAAAUCAGUGAAAGGCUUGACUCGGAAACAGG
..(((((....)))))....((((.(((((.......)))))(.(((..(((((.((((.....))))...((.....))----.-..............))))).))).).....)))) ( -31.90)
>consensus
AAGGGCUCCACAGCCCCAACCCUGAAAUGAAACACAGUCAUUGUGUCUUAGCCUGGCCAAAAACUGGCAUACCAAAAUGG____G_GGGAAAUCAGUGAAAGGCUUGACUCGGAAACAGG
..(((((....)))))(((.(((..............((((((..((((......((((.....))))...((.....))......))))...)))))).))).))).((((....)))) (-23.87 = -24.56 +   0.69)

alignment

secondary structure

dotplot

Window 2

Location	18,779,417 – 18,779,535
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	95.62
Mean single sequence MFE	-36.83
Consensus MFE	-35.67
Energy contribution	-35.42
Covariance contribution	-0.25
Combinations/Pair	1.11
Mean z-score	-1.58
Structure conservation index	0.97
SVM decision value	0.48
SVM RNA-class probability	0.751182
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18779417 118 + 22224390
CCUUUUUGGCAUGCCAGUUUUUGGCCAGGCUAAGACACAAUGACUGUAUUUCAUUUCAGGGUUGGGGCUGCGGAGCCCUUUUCUUCUUCGAGGAACCCUCGCAGAAAUUGUCAAACAA
...(((((((..(((((...)))))...))))))).....((((...(((((.....((((..((((((....))))))..))))...(((((...)))))..))))).))))..... ( -37.00)
>DroSec_CAF1 25910 118 + 1
CUAUUUUGGCAUGCCAGCUUUUGGCCAGGCUAAGACACAAUGACUGUGUUUCAUUUCAGGGUUGGGGCUGCGGAGCCCUUUUUUUCUUCGAGGAACCCUCGCAGAAAUUGUCAAACAA
.....(((((..(((((...)))))...)))))((((....((((.((........)).))))((((((....))))))...(((((.(((((...))))).))))).))))...... ( -37.20)
>DroEre_CAF1 24411 118 + 1
CCAUUUGGGUAUGCCAGUUUUUGGCCAGGCAAAGACACAAUGACUGUGUUUCAUUUCAGGGUUGGGGCUGUGGAGCCCUUUUCUUCUUCGAGGAACCCUCGCAGAAAUUGUCAAACAA
((....))....(((((...)))))..((((((((((((.....))))))).......(((..((((((....))))))..)))(((.(((((...))))).)))..)))))...... ( -35.00)
>DroYak_CAF1 24105 118 + 1
CCAUUUUGGUAUGCCAGUUUUUGGCCAGGCCAAGACACAAUGACUGUGUUUCAUUUCAGGGUUGGGGCUGUGGAGCCCUUUUCUUCUUCGAGGAACCCUCGCAGAAAUUGUCAAACAA
...(((((((..(((((...)))))...))))))).....((((...(((((.....((((..((((((....))))))..))))...(((((...)))))..))))).))))..... ( -38.10)
>consensus
CCAUUUUGGCAUGCCAGUUUUUGGCCAGGCUAAGACACAAUGACUGUGUUUCAUUUCAGGGUUGGGGCUGCGGAGCCCUUUUCUUCUUCGAGGAACCCUCGCAGAAAUUGUCAAACAA
...(((((((..(((((...)))))...))))))).....((((...(((((.....((((..((((((....))))))..))))...(((((...)))))..))))).))))..... (-35.67 = -35.42 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:54 2006