Locus 6715

Sequence ID dm3.chr3L
Location 9,146,308 – 9,146,406
Length 98
Max. P 0.999796
window9242 window9243

overview

Window 2

Location 9,146,308 – 9,146,406
Length 98
Sequences 8
Columns 109
Reading direction forward
Mean pairwise identity 58.10
Shannon entropy 0.84394
G+C content 0.39155
Mean single sequence MFE -27.06
Consensus MFE -22.62
Energy contribution -22.45
Covariance contribution -0.17
Combinations/Pair 1.52
Mean z-score -2.82
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.41
SVM RNA-class probability 0.999796
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9146308 98 + 24543557
----------AUUAUCUGGGUCGAUUUAUUUAUAUAUAUUUGUUUGGCAAUUUGGCAGCCUUCAUGUCUGGGUCACCCG-UUUAAGUGACCCAAACUUGAGAGCUCCAA
----------.........(((((..(((......))).....)))))...((((.(((.((((.((.((((((((...-.....)))))))).)).)))).))))))) ( -29.00, z-score =  -2.69, R)
>droSim1.chr3L_random 441398 105 + 1049610
AUUAUCUGGGUCGAUUUUUAUAUAU---UUUUUUGUUUUUUUUGUGGCGAUUUGGCAGCUUUCAUGUCUGGGUCACCCC-UUUAAGUGACCCAAACUUGAGAGCUCCAA
.........((((........(((.---.....)))........))))...((((.((((((((.((.((((((((...-.....)))))))).)).)))))))))))) ( -33.59, z-score =  -4.30, R)
>droSec1.super_0 1405126 106 + 21120651
UUUAUCUGGUUCGAUUU-UUUGUAUAUAUAUUUUGUUUU-UUUUUGGCAAUUUGGCAGCCUUCAUGUCUGGGUCACCCC-UUUAAGUGACCCAAACUUGAGAGCUCCAA
.................-..............(((((..-.....))))).((((.(((.((((.((.((((((((...-.....)))))))).)).)))).))))))) ( -27.70, z-score =  -2.75, R)
>droEre2.scaffold_4784 20861808 108 - 25762168
UUUAUCUGGUGCGAUUUUUUUGUACAUAUAUUGCUUUUUGUUUUUGGCAACUUGGCAGCCCUCAUGUCUGGGUCACCCC-UUUAAAUGACCCAAACUUAAUGGCUCCAA
........((((((.....)))))).....(((((..........)))))..(((.((((.....((.(((((((....-......))))))).)).....))))))). ( -29.70, z-score =  -2.78, R)
>dp4.chrXR_group5 356371 77 - 740492
-------------------------------AUUACCAAAUCUGGCUGGAUCUAGUAGCCAUCAUGUCUGGGUCACCCA-UUUAAGUGACCCAAACUUGAGGGCUCCAA
-------------------------------....(((........))).....(.((((.(((.((.((((((((...-.....)))))))).)).))).)))).).. ( -27.30, z-score =  -2.96, R)
>droPer1.super_58 22198 77 + 410386
-------------------------------AUUAACAAAUCUGGCUGGAUCUAGUAGCCAUCAUGUCUGGGUCACCCA-UUUAAGUGACCCAAACUUGAGGGCUCCAA
-------------------------------.............((((....))))((((.(((.((.((((((((...-.....)))))))).)).))).)))).... ( -26.10, z-score =  -2.72, R)
>droWil1.scaffold_181024 311294 102 - 1751709
-----AUUCUUAAGCUUCAUUCUCGUUUGUUUGUAUUGUAUUUGA--AAAUCUCAGAUCUAUUAUGUCUGGAUCACGUGCUUUAAGUGAUCCAAACUUAAUAGUUCGAA
-----.(((..(.((..((..(......)..))....)).)..))--).......((.((((((.((.((((((((.........)))))))).)).)))))).))... ( -22.30, z-score =  -2.76, R)
>droMoj3.scaffold_6680 24251231 91 - 24764193
--------------UUUAUAUAUAGAUAUUUAUUGCUUUGGCAUUAGCA--UUUGCGAUUGUCAUGUCUGCGACAUACA-UUCAAAUGCCACAGACUUGGCAAACCAA-
--------------..................((((....((....)).--...))))((((((.(((((.(.(((...-.....))).).))))).)))))).....- ( -20.80, z-score =  -1.59, R)
>consensus
_____________AUUU_UUU_UAU_UAUUUAUUAUUUUAUUUGUGGCAAUUUGGCAGCCAUCAUGUCUGGGUCACCCA_UUUAAGUGACCCAAACUUGAGAGCUCCAA
....................................................(((.((((((((.((.((((((((.........)))))))).)).))))))))))). (-22.62 = -22.45 +  -0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,146,308 – 9,146,406
Length 98
Sequences 8
Columns 109
Reading direction reverse
Mean pairwise identity 58.10
Shannon entropy 0.84394
G+C content 0.39155
Mean single sequence MFE -32.36
Consensus MFE -31.60
Energy contribution -29.15
Covariance contribution -2.45
Combinations/Pair 1.75
Mean z-score -4.79
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.63
SVM RNA-class probability 0.993579
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9146308 98 - 24543557
UUGGAGCUCUCAAGUUUGGGUCACUUAAA-CGGGUGACCCAGACAUGAAGGCUGCCAAAUUGCCAAACAAAUAUAUAUAAAUAAAUCGACCCAGAUAAU----------
(((((((..(((.((((((((((((....-..)))))))))))).)))..))).))))..........................(((......)))...---------- ( -34.70, z-score =  -5.51, R)
>droSim1.chr3L_random 441398 105 - 1049610
UUGGAGCUCUCAAGUUUGGGUCACUUAAA-GGGGUGACCCAGACAUGAAAGCUGCCAAAUCGCCACAAAAAAAACAAAAAA---AUAUAUAAAAAUCGACCCAGAUAAU
((((((((.(((.(((((((((((((...-.))))))))))))).))).)))).)))).......................---..........(((......)))... ( -34.60, z-score =  -5.95, R)
>droSec1.super_0 1405126 106 - 21120651
UUGGAGCUCUCAAGUUUGGGUCACUUAAA-GGGGUGACCCAGACAUGAAGGCUGCCAAAUUGCCAAAAA-AAAACAAAAUAUAUAUACAAA-AAAUCGAACCAGAUAAA
(((((((..(((.(((((((((((((...-.))))))))))))).)))..))).))))...........-.....................-..(((......)))... ( -35.00, z-score =  -5.62, R)
>droEre2.scaffold_4784 20861808 108 + 25762168
UUGGAGCCAUUAAGUUUGGGUCAUUUAAA-GGGGUGACCCAGACAUGAGGGCUGCCAAGUUGCCAAAAACAAAAAGCAAUAUAUGUACAAAAAAAUCGCACCAGAUAAA
((((((((.(((.(((((((((((((...-.))))))))))))).))).)))).))))(((((............)))))..............(((......)))... ( -34.40, z-score =  -3.88, R)
>dp4.chrXR_group5 356371 77 + 740492
UUGGAGCCCUCAAGUUUGGGUCACUUAAA-UGGGUGACCCAGACAUGAUGGCUACUAGAUCCAGCCAGAUUUGGUAAU-------------------------------
....((((.(((.(((((((((((((...-.))))))))))))).))).))))((((((((......))))))))...------------------------------- ( -37.60, z-score =  -5.78, R)
>droPer1.super_58 22198 77 - 410386
UUGGAGCCCUCAAGUUUGGGUCACUUAAA-UGGGUGACCCAGACAUGAUGGCUACUAGAUCCAGCCAGAUUUGUUAAU-------------------------------
....((((.(((.(((((((((((((...-.))))))))))))).))).))))..((((((......)))))).....------------------------------- ( -33.10, z-score =  -4.72, R)
>droWil1.scaffold_181024 311294 102 + 1751709
UUCGAACUAUUAAGUUUGGAUCACUUAAAGCACGUGAUCCAGACAUAAUAGAUCUGAGAUUU--UCAAAUACAAUACAAACAAACGAGAAUGAAGCUUAAGAAU-----
(((((.((((((.(((((((((((.........))))))))))).)))))).))((((((((--((...................))))))....)))).))).----- ( -25.11, z-score =  -4.66, R)
>droMoj3.scaffold_6680 24251231 91 + 24764193
-UUGGUUUGCCAAGUCUGUGGCAUUUGAA-UGUAUGUCGCAGACAUGACAAUCGCAAA--UGCUAAUGCCAAAGCAAUAAAUAUCUAUAUAUAAA--------------
-((((((((.((.(((((((((((.....-...))))))))))).)).)))..((...--.))....))))).......................-------------- ( -24.40, z-score =  -2.22, R)
>consensus
UUGGAGCUCUCAAGUUUGGGUCACUUAAA_GGGGUGACCCAGACAUGAAGGCUGCCAAAUUGCCAAAAAUAAAACAAAAAAUA_AUA_AAA_AAAU_____________
((((((((.(((.(((((((((((((.....))))))))))))).))).)))).))))................................................... (-31.60 = -29.15 +  -2.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:13:05 2011