Locus 13985

Sequence ID	dm3.chrX
Location	10,413,028 – 10,413,153
Length	125
Max. P	0.990346

overview

Window 3

Location	10,413,028 – 10,413,153
Length	125
Sequences	6
Columns	136
Reading direction	forward
Mean pairwise identity	73.11
Shannon entropy	0.50843
G+C content	0.48247
Mean single sequence MFE	-39.74
Consensus MFE	-19.62
Energy contribution	-20.45
Covariance contribution	0.83
Combinations/Pair	1.28
Mean z-score	-2.14
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.74
SVM RNA-class probability	0.964597
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10413028 125 + 22422827
CAGUGGUAAUUGCCACUUGGCUGCCACACAUGUGGCAAGU--CCUUCGA-----AUGGAGGCGACAAAUUUCA----GUUGGUUCUCCAAGGGAUUGCAAACUGAGUAAACUGCGCAAUGAACGGUGGCAAAUUAC
.....((((((((((((.(((((((((....))))).)))--)((((..-----..))))(((......((((----(((.((..(((...)))..)).))))))).......))).......)))))).)))))) ( -42.52, z-score =  -2.26, R)
>droSim1.chrX 8091574 122 + 17042790
---UGGUAAUUGCCACUUGGCUGCCACACAUGUGGCAAGU--CCUCCAA-----AUGGAGGCGACACAUUUCA----GUUGGUUCUCCAAGGGAUUGCAAACUGAGUGAACUGCGCAAUGAACGGUGGCAAAUUAC
---..((((((((((((.(((((((((....))))).)))--)((((..-----..))))(((......((((----(((.((..(((...)))..)).))))))).......))).......)))))).)))))) ( -46.12, z-score =  -3.09, R)
>droSec1.super_15 1120194 125 + 1954846
CAGUGGUAAUUGCCACUUGGCUGCCACACAUGUGGCAAGU--CCUCCGA-----AUGGAUGCGACAAAUUCAA----GUUGGUUCUCCAAGGGAUUGCAAACUGAGUAAACUGCGCAAUGAACGGUGGCAAAUUAC
.....((((((((((((.(((((((((....))))).)))--).(((..-----..)))((((.((.(((((.----(((.((..(((...)))..)).))))))))....))))))......)))))).)))))) ( -39.70, z-score =  -1.50, R)
>droYak2.chrX 18987064 107 + 21770863
CAGUGGUAAUUGCCACUUGGCU--------------------CCUCCGA-----AUGGAGGCGACAAAUUUCC----GUUGGUUCUCCAAGGGAUUGCAAACUGAGUAAACUGCUCAAUGAACGAUGGCAAAUUAC
.....((((((((((.(((((.--------------------(((((..-----..))))).........(((----.((((....)))).)))..))....(((((.....))))).....))))))).)))))) ( -33.10, z-score =  -2.20, R)
>droEre2.scaffold_4690 14036641 103 - 18748788
CAGUGGUAAUUGCCACUUGGCUGCCACACAUGUGGCAAGU--CCUCCAA-----AUGGAGGCGACAAAUUUCA----GUUGCUUCUCCAAGGGAUUGCAAACUGAGUAAACUAC----------------------
.((((((....))))))....((((((....)))))).(.--(((((..-----..)))))).......((((----(((((.(((.....)))..)).)))))))........---------------------- ( -36.40, z-score =  -2.85, R)
>droAna3.scaffold_13335 1047107 136 - 3335858
UACUGGUAAUUGGCACUUAGCUGGGGUAGCUGCCACAUGUGGCAGUAGAGGGUUAUGGAGGCGACAAAUGUCACAGGAGUGUGCCUCCAAGGAGUUGCAAGUUGGAUGGAGUUCGGGAUUUCGGGUAUGAAAUUAC
..((((...((..((..(((((...((((((((((....))))))).........((((((((((....)))(((....))))))))))......))).)))))..))))..))))(((((((....))))))).. ( -40.60, z-score =  -0.91, R)
>consensus
CAGUGGUAAUUGCCACUUGGCUGCCACACAUGUGGCAAGU__CCUCCGA_____AUGGAGGCGACAAAUUUCA____GUUGGUUCUCCAAGGGAUUGCAAACUGAGUAAACUGCGCAAUGAACGGUGGCAAAUUAC
((((.(((((((((....)))((((((....))))))..................((((((((((............))))..))))))...))))))..))))................................ (-19.62 = -20.45 +   0.83)

alignment

secondary structure

dotplot

Window 4

Location	10,413,028 – 10,413,153
Length	125
Sequences	6
Columns	136
Reading direction	reverse
Mean pairwise identity	73.11
Shannon entropy	0.50843
G+C content	0.48247
Mean single sequence MFE	-36.87
Consensus MFE	-16.73
Energy contribution	-19.97
Covariance contribution	3.24
Combinations/Pair	1.17
Mean z-score	-2.71
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.41
SVM RNA-class probability	0.990346
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10413028 125 - 22422827
GUAAUUUGCCACCGUUCAUUGCGCAGUUUACUCAGUUUGCAAUCCCUUGGAGAACCAAC----UGAAAUUUGUCGCCUCCAU-----UCGAAGG--ACUUGCCACAUGUGUGGCAGCCAAGUGGCAAUUACCACUG
((((((.(((((((......((((((.....((((((.(...(((...)))...).)))----)))...))).)))......-----.))..((--.((.(((((....)))))))))..)))))))))))..... ( -37.62, z-score =  -2.30, R)
>droSim1.chrX 8091574 122 - 17042790
GUAAUUUGCCACCGUUCAUUGCGCAGUUCACUCAGUUUGCAAUCCCUUGGAGAACCAAC----UGAAAUGUGUCGCCUCCAU-----UUGGAGG--ACUUGCCACAUGUGUGGCAGCCAAGUGGCAAUUACCA---
((((((.(((((........(((((......((((((.(...(((...)))...).)))----)))..)))))..(((((..-----..)))))--..(((((((....)))))))....)))))))))))..--- ( -41.80, z-score =  -2.59, R)
>droSec1.super_15 1120194 125 - 1954846
GUAAUUUGCCACCGUUCAUUGCGCAGUUUACUCAGUUUGCAAUCCCUUGGAGAACCAAC----UUGAAUUUGUCGCAUCCAU-----UCGGAGG--ACUUGCCACAUGUGUGGCAGCCAAGUGGCAAUUACCACUG
((((((.(((((.((((..(((((((.....((((.(((...(((...)))....))).----))))..))).))))(((..-----..)))))--))(((((((....)))))))....)))))))))))..... ( -39.10, z-score =  -2.25, R)
>droYak2.chrX 18987064 107 - 21770863
GUAAUUUGCCAUCGUUCAUUGAGCAGUUUACUCAGUUUGCAAUCCCUUGGAGAACCAAC----GGAAAUUUGUCGCCUCCAU-----UCGGAGG--------------------AGCCAAGUGGCAAUUACCACUG
((((((.(((...((..((((((.......))))))..))..(((.((((....)))).----))).(((((.(.(((((..-----..)))))--------------------.).))))))))))))))..... ( -34.50, z-score =  -3.26, R)
>droEre2.scaffold_4690 14036641 103 + 18748788
----------------------GUAGUUUACUCAGUUUGCAAUCCCUUGGAGAAGCAAC----UGAAAUUUGUCGCCUCCAU-----UUGGAGG--ACUUGCCACAUGUGUGGCAGCCAAGUGGCAAUUACCACUG
----------------------((((((...((((((.((..(((...)))...)))))----))).........(((((..-----..)))))--...((((((....))))))(((....)))))))))..... ( -34.80, z-score =  -2.44, R)
>droAna3.scaffold_13335 1047107 136 + 3335858
GUAAUUUCAUACCCGAAAUCCCGAACUCCAUCCAACUUGCAACUCCUUGGAGGCACACUCCUGUGACAUUUGUCGCCUCCAUAACCCUCUACUGCCACAUGUGGCAGCUACCCCAGCUAAGUGCCAAUUACCAGUA
(..(((((......)))))..)............((((((.......((((((((((....)))(((....))))))))))..........((((((....))))))........)).)))).............. ( -33.40, z-score =  -3.44, R)
>consensus
GUAAUUUGCCACCGUUCAUUGCGCAGUUUACUCAGUUUGCAAUCCCUUGGAGAACCAAC____UGAAAUUUGUCGCCUCCAU_____UCGGAGG__ACUUGCCACAUGUGUGGCAGCCAAGUGGCAAUUACCACUG
((((((.((((...........((((..........)))).....(((((.........................(((((.........))))).....((((((....)))))).)))))))))))))))..... (-16.73 = -19.97 +   3.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:31:27 2011