Locus 13458

Sequence ID dm3.chrX
Location 6,664,857 – 6,664,955
Length 98
Max. P 0.663157
window18536 window18537

overview

Window 6

Location 6,664,857 – 6,664,955
Length 98
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 52.49
Shannon entropy 0.76014
G+C content 0.46426
Mean single sequence MFE -29.05
Consensus MFE -10.21
Energy contribution -9.28
Covariance contribution -0.94
Combinations/Pair 1.61
Mean z-score -1.13
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.663157
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6664857 98 + 22422827
--------AUCACGCAUUUGAAUCCACCGCGCCACAAUCUCCUAGCGGG-UAGUUACCCGGGACGAUUGUGGUAAUUUUCA-UUGAGAUACACAUAGA---AUCC-----GCAUUU
--------....................((((((((((((((...((((-(....)))))))).)))))))))........-..(.(((.(.....).---))))-----)).... ( -26.30, z-score =  -1.90, R)
>droEre2.scaffold_4690 15593060 114 + 18748788
AGUGACGAGUCUCGCACUUGAAUCCACCCCGCCCCAAUCUCCUAGCGGGGAGGAAAUCCGG-AGGAUCGUGGUGAAGUUCA-UCGAGAUAUGUAUAUAUACAUUGAAUACGCAUUA
((((.((.((((((....(((((.((((.((((((..(((((....)))))((....))))-.))..)).))))..)))))-.))))))(((((....)))))......)))))). ( -33.70, z-score =  -1.02, R)
>droYak2.chrX 2629199 100 + 21770863
--------AUCACGCAUUGGAAACCACCCGGCGC-AAUCCCCCAGCGGGGCGGCAGGCCGGGAGGAUCGUGGUGAAAUUCA-UCGAGAUACACGUAGA---AUUUAA---GCAUUA
--------.....((.(((((..((.((((((((-...((((....))))..))..)))))).))(((.(((((.....))-))).))).........---.)))))---)).... ( -34.10, z-score =  -1.40, R)
>droAna3.scaffold_13117 4449852 104 + 5790199
--------AGCAAGUAUUUAUACCAUCUGCGGCAGAUGCUUCUGCAAGGGUUAUCAUCUACUUAUAUAGAUGUCAUCUAUAGCCUUGUUGUAAACAAACAUAGUCUUGAUGA----
--------...............((((.((.(((((....))))).((((((((((((((......))))))......))))))))................))...)))).---- ( -22.10, z-score =  -0.19, R)
>consensus
________AUCACGCAUUUGAAUCCACCCCGCCACAAUCUCCUAGCGGGGUGGUAAUCCGGGAGGAUCGUGGUGAAAUUCA_UCGAGAUACACAUAGA___AUUCAA___GCAUUA
........((((((....((((.((((..........(((((....)))))....((((....)))).)))).....))))..))))))........................... (-10.21 =  -9.28 +  -0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,664,857 – 6,664,955
Length 98
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 52.49
Shannon entropy 0.76014
G+C content 0.46426
Mean single sequence MFE -29.75
Consensus MFE -10.43
Energy contribution -12.43
Covariance contribution 2.00
Combinations/Pair 1.56
Mean z-score -1.08
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.618146
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6664857 98 - 22422827
AAAUGC-----GGAU---UCUAUGUGUAUCUCAA-UGAAAAUUACCACAAUCGUCCCGGGUAACUA-CCCGCUAGGAGAUUGUGGCGCGGUGGAUUCAAAUGCGUGAU--------
..((((-----.((.---((((((((......((-(....))).((((((((.((((((((....)-))))...)))))))))))))).))))).))....))))...-------- ( -32.00, z-score =  -2.35, R)
>droEre2.scaffold_4690 15593060 114 - 18748788
UAAUGCGUAUUCAAUGUAUAUAUACAUAUCUCGA-UGAACUUCACCACGAUCCU-CCGGAUUUCCUCCCCGCUAGGAGAUUGGGGCGGGGUGGAUUCAAGUGCGAGACUCGUCACU
..((((((.....)))))).............((-(((..(((..((((((((.-..)))))(((.(((((((..........))))))).))).....))).)))..)))))... ( -32.80, z-score =  -0.46, R)
>droYak2.chrX 2629199 100 - 21770863
UAAUGC---UUAAAU---UCUACGUGUAUCUCGA-UGAAUUUCACCACGAUCCUCCCGGCCUGCCGCCCCGCUGGGGGAUU-GCGCCGGGUGGUUUCCAAUGCGUGAU--------
......---......---..(((((((...(((.-((........))))).((.((((((..((..((((....))))...-)))))))).))......)))))))..-------- ( -32.20, z-score =  -0.74, R)
>droAna3.scaffold_13117 4449852 104 - 5790199
----UCAUCAAGACUAUGUUUGUUUACAACAAGGCUAUAGAUGACAUCUAUAUAAGUAGAUGAUAACCCUUGCAGAAGCAUCUGCCGCAGAUGGUAUAAAUACUUGCU--------
----(((((.((.((.((((.(....))))).))))...)))))(((((((....))))))).........(((((....))))).(((...((((....))))))).-------- ( -22.00, z-score =  -0.77, R)
>consensus
UAAUGC___UUGAAU___UCUAUGUAUAUCUCGA_UGAAAAUCACCACGAUCCUCCCGGAUUACCACCCCGCUAGGAGAUUGGGGCGCGGUGGAUUCAAAUGCGUGAU________
............................(((((..((((.........(((((....))))).(((((((((((........))))))))))).))))....)))))......... (-10.43 = -12.43 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:50 2011