Locus 12849

Sequence ID dm3.chrX
Location 2,623,817 – 2,623,933
Length 116
Max. P 0.731978
window17667 window17668

overview

Window 7

Location 2,623,817 – 2,623,933
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 57.70
Shannon entropy 0.55414
G+C content 0.61381
Mean single sequence MFE -40.07
Consensus MFE -26.05
Energy contribution -25.07
Covariance contribution -0.98
Combinations/Pair 1.44
Mean z-score -0.69
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.731978
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2623817 116 + 22422827
CAUCAAUCCUCCCAGCCGACAAGCGGGCGCAGAAGGUGCGACAGGCGGAGGUGCGACAGGUGGAAGUCCGACCGGUGGAGGUGCGACCGGUGGAUCGGCAACCAACCUUCACAUAA
.......((((((..(((.....)))((((.....)))).....).)))))((.((.((((((..((((.((((((.(.....).)))))).)...)))..)).)))))).))... ( -39.00, z-score =   0.83, R)
>dp4.chrXL_group1e 2015352 99 + 12523060
-------------CUUCGGCA-GUGGGCGUGGGCG-UG-GGCAUGCAUGUGACCAAUGAUCUCAACCACCGUCA-UGGCGGUGGAGGAGGAGGAUCCUCUACGGUCAUGCAUUCGG
-------------...(((((-((..(((....))-).-.)).)))..((((((......(((..(((((((..-..)))))))..)))(((....)))...)))))).....)). ( -38.60, z-score =  -0.84, R)
>droPer1.super_18 865939 99 + 1952607
-------------CUUCGGCA-GUCGGCGUGGGCG-UG-GGCAUGCAUGUGACCAAUGAUCUCAACCACCGUCA-UGGCGGUGGAGGAGGAGGAUCCUCUACGGUCAUGCAUUCGG
-------------...(((((-(((.(((....))-).-))).)))..((((((......(((..(((((((..-..)))))))..)))(((....)))...)))))).....)). ( -42.60, z-score =  -2.06, R)
>consensus
_____________CUUCGGCA_GUGGGCGUGGGCG_UG_GGCAUGCAUGUGACCAAUGAUCUCAACCACCGUCA_UGGCGGUGGAGGAGGAGGAUCCUCUACGGUCAUGCAUUCGG
..........................(((((..........))))).(((((((......(((..(((((((.....)))))))..)))(((....)))...)))))))....... (-26.05 = -25.07 +  -0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 2,623,817 – 2,623,933
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 57.70
Shannon entropy 0.55414
G+C content 0.61381
Mean single sequence MFE -34.03
Consensus MFE -16.67
Energy contribution -17.23
Covariance contribution 0.57
Combinations/Pair 1.33
Mean z-score -1.04
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chrX 2623817 116 - 22422827
UUAUGUGAAGGUUGGUUGCCGAUCCACCGGUCGCACCUCCACCGGUCGGACUUCCACCUGUCGCACCUCCGCCUGUCGCACCUUCUGCGCCCGCUUGUCGGCUGGGAGGAUUGAUG
...(((((((((.((...((((....(((((.(.....).)))))))))....)))))).)))))(((((.......(((.....)))(((........)))..)))))....... ( -38.50, z-score =   0.28, R)
>dp4.chrXL_group1e 2015352 99 - 12523060
CCGAAUGCAUGACCGUAGAGGAUCCUCCUCCUCCACCGCCA-UGACGGUGGUUGAGAUCAUUGGUCACAUGCAUGCC-CA-CGCCCACGCCCAC-UGCCGAAG-------------
.((.(((((((((((..((((.....))))(((.((((((.-....)))))).))).....))))))..)))))((.-..-.((....))....-.))))...------------- ( -31.80, z-score =  -1.80, R)
>droPer1.super_18 865939 99 - 1952607
CCGAAUGCAUGACCGUAGAGGAUCCUCCUCCUCCACCGCCA-UGACGGUGGUUGAGAUCAUUGGUCACAUGCAUGCC-CA-CGCCCACGCCGAC-UGCCGAAG-------------
.((.(((((((((((..((((.....))))(((.((((((.-....)))))).))).....))))))..)))))((.-..-.((....))....-.))))...------------- ( -31.80, z-score =  -1.60, R)
>consensus
CCGAAUGCAUGACCGUAGAGGAUCCUCCUCCUCCACCGCCA_UGACGGUGGUUGAGAUCAUUGGUCACAUGCAUGCC_CA_CGCCCACGCCCAC_UGCCGAAG_____________
....(((((((((((..((((.....))))(((.((((((......)))))).))).....))))))..))))).......................................... (-16.67 = -17.23 +   0.57)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:09:59 2011