Locus 11876

Sequence ID dm3.chr3R
Location 24,331,286 – 24,331,397
Length 111
Max. P 0.960343
window16324 window16325 window16326

overview

Window 4

Location 24,331,286 – 24,331,384
Length 98
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 71.63
Shannon entropy 0.48522
G+C content 0.36083
Mean single sequence MFE -23.00
Consensus MFE -13.98
Energy contribution -13.38
Covariance contribution -0.60
Combinations/Pair 1.31
Mean z-score -1.71
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.951806
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24331286 98 + 27905053
------------GUUGUUA--CCUCAACAUGGC--UGUAAUACAUUGUAGUGUAAACUAAAAAUGAAUGUCCAUGAGAUUCGGGCAAUUUUUUAUUGUGUGAAUCCCUGCUGAU
------------.......--..(((.(((((.--....((.((((.((((....))))..)))).))..))))).((((((.(((((.....))))).)))))).....))). ( -21.10, z-score =  -1.14, R)
>droSim1.chr3R 24021117 105 + 27517382
---------GUUGUUACCAUGUUGAGGUAAUACCUUGUAAUGCCUUGUAGGGUAAACUAAAAAAGAAUGUCCAUAAGAUUCGGUCAAUUUUUUAUUGAGUGAAUCCCUGCUGAU
---------....(((((....(((((((.(((...))).)))))))...))))).....................((((((.(((((.....))))).))))))......... ( -23.90, z-score =  -1.93, R)
>droSec1.super_22 934403 105 + 1066717
---------GUUGUUACCAUGUUGAGGUAAUACCUUGUAAUGCCUUGUAGGGUAAACUAAAAAAGAAUGUCCAGGAGAUUCGGUCAAUAUUUUAUUGAGUGAAUCCCUGCUGAU
---------....(((((....(((((((.(((...))).)))))))...)))))................((((.((((((.((((((...)))))).))))))))))..... ( -30.50, z-score =  -3.46, R)
>droYak2.chr3R 6665660 87 - 28832112
-------------------------AACAUGAU--UUUAAUACUUUGUAGGGUAAACUAAAACGGUAUUUCCAUGAGACUCGGACAAUUUUUUAUUGAGCGAAUCCCUGCUGAU
-------------------------........--...........((((((...........((.....)).......(((..((((.....))))..)))..)))))).... ( -14.10, z-score =  -0.17, R)
>droEre2.scaffold_4820 6763072 111 - 10470090
GUUGUUAUAUUCCUAGCUAACCCUCAACAUGAC--UCUAAUACUGGCUAGGGUAAACUAAAA-AGUAUUUCCAUGAGAUUCGGUCAAUUUUUUAUUGAGCGAAUCCCUGCAGAG
(((((((......)))).))).(((..((((..--...((((((...(((......)))...-))))))..)))).((((((.(((((.....))))).))))))......))) ( -25.40, z-score =  -1.83, R)
>consensus
__________U_GUUACCA__CCGAAACAUGAC__UGUAAUACCUUGUAGGGUAAACUAAAAAAGAAUGUCCAUGAGAUUCGGUCAAUUUUUUAUUGAGUGAAUCCCUGCUGAU
........................................(((((....)))))......................((((((.(((((.....))))).))))))......... (-13.98 = -13.38 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,331,286 – 24,331,384
Length 98
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 71.63
Shannon entropy 0.48522
G+C content 0.36083
Mean single sequence MFE -20.32
Consensus MFE -10.16
Energy contribution -10.00
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -1.61
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.745169
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24331286 98 - 27905053
AUCAGCAGGGAUUCACACAAUAAAAAAUUGCCCGAAUCUCAUGGACAUUCAUUUUUAGUUUACACUACAAUGUAUUACA--GCCAUGUUGAGG--UAACAAC------------
.(((((.(((((((...((((.....))))...)))))))((((.....((((..((((....)))).)))).......--.)))))))))..--.......------------ ( -19.62, z-score =  -1.88, R)
>droSim1.chr3R 24021117 105 - 27517382
AUCAGCAGGGAUUCACUCAAUAAAAAAUUGACCGAAUCUUAUGGACAUUCUUUUUUAGUUUACCCUACAAGGCAUUACAAGGUAUUACCUCAACAUGGUAACAAC---------
....((.(((((((..(((((.....)))))..))))))).(((((...........))))).........))...........(((((.......)))))....--------- ( -15.90, z-score =  -0.36, R)
>droSec1.super_22 934403 105 - 1066717
AUCAGCAGGGAUUCACUCAAUAAAAUAUUGACCGAAUCUCCUGGACAUUCUUUUUUAGUUUACCCUACAAGGCAUUACAAGGUAUUACCUCAACAUGGUAACAAC---------
(((..(((((((((..((((((...))))))..))))).))))..............((....((.....))....))..))).(((((.......)))))....--------- ( -20.50, z-score =  -1.67, R)
>droYak2.chr3R 6665660 87 + 28832112
AUCAGCAGGGAUUCGCUCAAUAAAAAAUUGUCCGAGUCUCAUGGAAAUACCGUUUUAGUUUACCCUACAAAGUAUUAAA--AUCAUGUU-------------------------
...((((((((((((..((((.....))))..)))))))).....(((((..((.(((......))).)).)))))...--....))))------------------------- ( -16.30, z-score =  -1.78, R)
>droEre2.scaffold_4820 6763072 111 + 10470090
CUCUGCAGGGAUUCGCUCAAUAAAAAAUUGACCGAAUCUCAUGGAAAUACU-UUUUAGUUUACCCUAGCCAGUAUUAGA--GUCAUGUUGAGGGUUAGCUAGGAAUAUAACAAC
.......((((((((.(((((.....))))).)))))))).((...(((.(-((((((((.(((((...((........--....))...))))).))))))))))))..)).. ( -29.30, z-score =  -2.36, R)
>consensus
AUCAGCAGGGAUUCACUCAAUAAAAAAUUGACCGAAUCUCAUGGACAUUCUUUUUUAGUUUACCCUACAAAGUAUUACA__GUCAUGUUGAAA__UAGCAAC_A__________
....((.(((((((..(((((.....)))))..)))))))...............(((......)))....))......................................... (-10.16 = -10.00 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,331,297 – 24,331,397
Length 100
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 65.47
Shannon entropy 0.64849
G+C content 0.39448
Mean single sequence MFE -24.47
Consensus MFE -9.95
Energy contribution -10.15
Covariance contribution 0.20
Combinations/Pair 1.50
Mean z-score -1.84
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24331297 100 + 27905053
------------AACAUGGCUGUAAUACAUUGUAGUGUAAACUAAAAAUGAAUGUCCAUGAGAUUCGGGCAAUUUUUUAUUGUGUGAAUCCCUGCUGAUUUUCGUAUCCAAG
------------....(((......(((((....)))))........(((((.(((((.(.((((((.(((((.....))))).))))))).))..))).)))))..))).. ( -21.30, z-score =  -1.32, R)
>droSim1.chr3R 24021128 107 + 27517382
----GUUGAGGUAAUACC-UUGUAAUGCCUUGUAGGGUAAACUAAAAAAGAAUGUCCAUAAGAUUCGGUCAAUUUUUUAUUGAGUGAAUCCCUGCUGAUUUUCGUAUCCAAG
----...((((((.(((.-..))).))))))...(((((..........(((.(((.....((((((.(((((.....))))).))))))......))).))).)))))... ( -24.60, z-score =  -2.16, R)
>droSec1.super_22 934414 107 + 1066717
----GUUGAGGUAAUACC-UUGUAAUGCCUUGUAGGGUAAACUAAAAAAGAAUGUCCAGGAGAUUCGGUCAAUAUUUUAUUGAGUGAAUCCCUGCUGAUUUUCGUAUCCGAG
----...((((((.(((.-..))).))))))...(((((..........(((.(((((((.((((((.((((((...)))))).))))))))))..))).))).)))))... ( -31.80, z-score =  -3.71, R)
>droYak2.chr3R 6665660 100 - 28832112
------------AACAUGAUUUUAAUACUUUGUAGGGUAAACUAAAACGGUAUUUCCAUGAGACUCGGACAAUUUUUUAUUGAGCGAAUCCCUGCUGAUUUUCGUAUCCAAG
------------..((((.....((((((...(((......)))....))))))..))))......(((((((.....)))).(((((............))))).)))... ( -15.60, z-score =   0.32, R)
>droEre2.scaffold_4820 6763085 111 - 10470090
UAGCUAACCCUCAACAUGACUCUAAUACUGGCUAGGGUAAACUAAAA-AGUAUUUCCAUGAGAUUCGGUCAAUUUUUUAUUGAGCGAAUCCCUGCAGAGUUUCGUAUCCAAG
.............((..((((((((((((...(((......)))...-))))))..((.(.((((((.(((((.....))))).))))))).)).))))))..))....... ( -25.80, z-score =  -1.94, R)
>droVir3.scaffold_12822 3771643 85 + 4096053
--------------------GCCGAGGCAUUGCC-UAUCGGCAAUAACUGAACAUACUCUGUCUCCUGGCAACUCUUU------UGGUUACUCGGGCAUUUGGCCCGCCGAG
--------------------((((((((((((((-....))))))....((......)).)))))..))).......(------(((.....(((((.....))))))))). ( -27.70, z-score =  -2.21, R)
>consensus
____________AACAUG_UUGUAAUACAUUGUAGGGUAAACUAAAAAAGAAUGUCCAUGAGAUUCGGUCAAUUUUUUAUUGAGUGAAUCCCUGCUGAUUUUCGUAUCCAAG
.........................(((((....)))))......................((((((.(((((.....))))).))))))...................... ( -9.95 = -10.15 +   0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:51:23 2011