Locus 14802

Sequence ID	dm3.chrX
Location	15,571,475 – 15,571,566
Length	91
Max. P	0.756532

overview

Window 1

Location	15,571,475 – 15,571,566
Length	91
Sequences	11
Columns	103
Reading direction	forward
Mean pairwise identity	64.38
Shannon entropy	0.76163
G+C content	0.65198
Mean single sequence MFE	-34.47
Consensus MFE	-12.58
Energy contribution	-13.35
Covariance contribution	0.77
Combinations/Pair	1.38
Mean z-score	-0.95
Structure conservation index	0.36
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.12
SVM RNA-class probability	0.553867
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 15571475 91 + 22422827
GUGGGCACAAUUCCACCAGCGACUGCGAGCUGGAGGAGGAGCA------------CUGCCAGCUGAGUCGCGGACUGGAGUUGGGUGGCGAGGAGCUGGAGGA
....((.((((((((((.((((((.(.((((((((........------------)).)))))))))))))))..)))))))).))(((.....)))...... ( -36.50, z-score =  -1.11, R)
>droSim1.chrX 12065845 91 + 17042790
GUGGGCACAAUUCCACCAGCGACUGCGAGCUGGAGGAGGAGCA------------CUGCCAGCUGAGCCGCGGACUGGAGUUGGGUGGCGAGGAGCUGGAGGA
....((....((((.(((((........))))).))))..)).------------((.((((((..(((((.(((....))).).))))....)))))).)). ( -36.30, z-score =  -0.83, R)
>droSec1.super_37 149746 91 + 454039
GUGGGCACAAUUCCACCAGCGACUGCGAGCUGGAGGAGGAGCA------------CUGCCAGCUGAGUCGCGGCCUGGAGUUGGGUGGCGAGGAGCUGGAGGA
....((....((((.(((((........))))).))))..)).------------((.((((((...((((.((((......)))).))))..)))))).)). ( -40.20, z-score =  -1.52, R)
>droYak2.chrX 9766598 91 + 21770863
GUGGGCACAACUCCACCAGCGACUUGGAGCUGGAGGAGGAGCA------------CUGCCAGCUGAGCCGCGGCUUGGAAUUGGGUGGCGAGGAGCUGGAGGA
....((....((((.(((((........))))).))))..)).------------((.((((((....(((.((((......)))).)))...)))))).)). ( -37.50, z-score =  -1.21, R)
>droEre2.scaffold_4690 7278535 91 - 18748788
GUGGGCACAACUCCACCAGCGACUGUGAGCUGGAGGAGGAGCA------------CUGCCAGCUGAGCCGCGGAUUGGAAUUGGGUGGCGAGGAGCUGGAGGA
....((....((((.(((((........))))).))))..)).------------((.((((((..(((((.............)))))....)))))).)). ( -36.52, z-score =  -1.56, R)
>droAna3.scaffold_12929 578278 70 - 3277472
GCGGGCACAACUCCACCACCGACCUGGAG---GAGGAGGAGCA----------------------GGCCG--------GACUGGGUGGCGAGGAGUUGGAAGC
((...(.(((((((.(((((..(((....---.))).....((----------------------(....--------..))))))))...))))))))..)) ( -25.90, z-score =  -0.79, R)
>dp4.chrXL_group1a 1146289 103 - 9151740
GCGGCCACAACUCGACCAGCGACUGCGAGCUGGACGAGGAGCAUCCGAUUCCCAUUCUGGCAAUGGGAUUGGGAUUGGGACUGGGCGGCGAGGAGCUGGAAGC
((.(((.((.((((.(((((........))))).)))).....(((((((((.(((((......))))).)))))))))..))))).)).............. ( -41.50, z-score =  -1.91, R)
>droPer1.super_15 1818709 103 - 2181545
GCGGCCACAACUCGACCAGCGACUGCGAGCUGGACGAGGAGCAUCCGAUUCCCAUGCUGGCAAUGGGAUUGGGAUUGGGACUGGGCGGCGAGGAGCUGGAAGC
((.(((.((.((((.(((((........))))).))))....((((.(.((((((.......)))))).).))))......))))).)).............. ( -40.20, z-score =  -1.45, R)
>droVir3.scaffold_13042 1598167 88 + 5191987
GCGGACACAAUUCCACCAGCGACUGCGAGCUGGAACUGGACGA---------------GGAGAAGGAUGAGAACCUGGCGCUGGGCAAGCCGCAGCUGGAGGG
............((.(((((...((((.(((....(..(.((.---------------.....(((.......)))..)))..)...)))))))))))).)). ( -27.20, z-score =  -0.04, R)
>droGri2.scaffold_15081 2549770 100 + 4274704
GCGGACACAACUCCACCAGCGACUGCGAGCUGGAGGAGGAG---CUGGGCUUAAGAGCAGGAACGGGUCUGGAACUGGUACUUGGUGGAGAGGAGCUGGAGGC
.(((((....((((.(((((........))))).))))...---(((..(((......)))..))))))))...(..((.(((......)))..))..).... ( -33.20, z-score =  -0.49, R)
>anoGam1.chr2R 36355598 78 - 62725911
GCACACACUUCUCCACCACGCUCAGCCCGC-GGGCCAGAUGUU-----------------CGACGGGGCCGAGCAGGCUCUCCAGCACCACCGGGC-------
...............((..((((.((((.(-((((.....)))-----------------))...)))).))))..(((....)))......))..------- ( -24.20, z-score =   0.42, R)
>consensus
GCGGGCACAACUCCACCAGCGACUGCGAGCUGGAGGAGGAGCA____________CUGCCAGAUGGGCCGCGGACUGGAAUUGGGUGGCGAGGAGCUGGAGGA
..........((((.(((((........))))).))))...............................................((((.....))))..... (-12.58 = -13.35 +   0.77)

alignment

secondary structure

dotplot

Window 2

Location	15,571,475 – 15,571,566
Length	91
Sequences	11
Columns	103
Reading direction	reverse
Mean pairwise identity	64.38
Shannon entropy	0.76163
G+C content	0.65198
Mean single sequence MFE	-29.83
Consensus MFE	-9.24
Energy contribution	-9.83
Covariance contribution	0.59
Combinations/Pair	1.25
Mean z-score	-1.48
Structure conservation index	0.31
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.60
SVM RNA-class probability	0.756532
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 15571475 91 - 22422827
UCCUCCAGCUCCUCGCCACCCAACUCCAGUCCGCGACUCAGCUGGCAG------------UGCUCCUCCUCCAGCUCGCAGUCGCUGGUGGAAUUGUGCCCAC
.......((.(....(((((..((....))..(((((((((((((.((------------........)))))))).).)))))).)))))....).)).... ( -28.80, z-score =  -1.69, R)
>droSim1.chrX 12065845 91 - 17042790
UCCUCCAGCUCCUCGCCACCCAACUCCAGUCCGCGGCUCAGCUGGCAG------------UGCUCCUCCUCCAGCUCGCAGUCGCUGGUGGAAUUGUGCCCAC
....((((((....(((.(...((....))..).)))..))))))..(------------..(...(((.(((((........))))).)))...)..).... ( -28.80, z-score =  -1.17, R)
>droSec1.super_37 149746 91 - 454039
UCCUCCAGCUCCUCGCCACCCAACUCCAGGCCGCGACUCAGCUGGCAG------------UGCUCCUCCUCCAGCUCGCAGUCGCUGGUGGAAUUGUGCCCAC
....((((((..((((..((........))..))))...))))))..(------------..(...(((.(((((........))))).)))...)..).... ( -32.00, z-score =  -1.89, R)
>droYak2.chrX 9766598 91 - 21770863
UCCUCCAGCUCCUCGCCACCCAAUUCCAAGCCGCGGCUCAGCUGGCAG------------UGCUCCUCCUCCAGCUCCAAGUCGCUGGUGGAGUUGUGCCCAC
....((((((....(((.(.............).)))..))))))..(------------..(..((((.(((((........))))).))))..)..).... ( -31.62, z-score =  -2.25, R)
>droEre2.scaffold_4690 7278535 91 + 18748788
UCCUCCAGCUCCUCGCCACCCAAUUCCAAUCCGCGGCUCAGCUGGCAG------------UGCUCCUCCUCCAGCUCACAGUCGCUGGUGGAGUUGUGCCCAC
....((((((....(((.(.............).)))..))))))..(------------..(..((((.(((((........))))).))))..)..).... ( -31.62, z-score =  -2.73, R)
>droAna3.scaffold_12929 578278 70 + 3277472
GCUUCCAACUCCUCGCCACCCAGUC--------CGGCC----------------------UGCUCCUCCUC---CUCCAGGUCGGUGGUGGAGUUGUGCCCGC
((...(((((((..((((((.....--------.((((----------------------((.........---...))))))))))))))))))).)).... ( -26.40, z-score =  -2.54, R)
>dp4.chrXL_group1a 1146289 103 + 9151740
GCUUCCAGCUCCUCGCCGCCCAGUCCCAAUCCCAAUCCCAUUGCCAGAAUGGGAAUCGGAUGCUCCUCGUCCAGCUCGCAGUCGCUGGUCGAGUUGUGGCCGC
((.....)).....((.(((........((((...(((((((.....)))))))...))))((..((((.(((((........))))).))))..))))).)) ( -36.80, z-score =  -2.30, R)
>droPer1.super_15 1818709 103 + 2181545
GCUUCCAGCUCCUCGCCGCCCAGUCCCAAUCCCAAUCCCAUUGCCAGCAUGGGAAUCGGAUGCUCCUCGUCCAGCUCGCAGUCGCUGGUCGAGUUGUGGCCGC
((.....)).....((.(((........((((...((((((.(....)))))))...))))((..((((.(((((........))))).))))..))))).)) ( -35.90, z-score =  -1.89, R)
>droVir3.scaffold_13042 1598167 88 - 5191987
CCCUCCAGCUGCGGCUUGCCCAGCGCCAGGUUCUCAUCCUUCUCC---------------UCGUCCAGUUCCAGCUCGCAGUCGCUGGUGGAAUUGUGUCCGC
.(((...((((.((....))))))...)))...............---------------..(.(((((((((.((.((....)).)))))))))).).)... ( -24.70, z-score =  -0.23, R)
>droGri2.scaffold_15081 2549770 100 - 4274704
GCCUCCAGCUCCUCUCCACCAAGUACCAGUUCCAGACCCGUUCCUGCUCUUAAGCCCAG---CUCCUCCUCCAGCUCGCAGUCGCUGGUGGAGUUGUGUCCGC
.......((.(..((((((((.((..(.....(((........))).......((..((---((........)))).)).)..))))))))))..).)).... ( -22.10, z-score =  -0.24, R)
>anoGam1.chr2R 36355598 78 + 62725911
-------GCCCGGUGGUGCUGGAGAGCCUGCUCGGCCCCGUCG-----------------AACAUCUGGCCC-GCGGGCUGAGCGUGGUGGAGAAGUGUGUGC
-------..((((.....))))...((((((((((((((((((-----------------......))))..-).)))))))))).))).............. ( -29.40, z-score =   0.68, R)
>consensus
UCCUCCAGCUCCUCGCCACCCAAUUCCAGUCCCCGACCCAGCUGGCAG____________UGCUCCUCCUCCAGCUCGCAGUCGCUGGUGGAGUUGUGCCCGC
..................................................................(((.(((((........))))).)))........... ( -9.24 =  -9.83 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:46:57 2011