Locus 8540

Sequence ID dm3.chr3RHet
Location 183,161 – 183,310
Length 149
Max. P 0.983240
window11731 window11732 window11733 window11734

overview

Window 1

Location 183,161 – 183,270
Length 109
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 55.08
Shannon entropy 0.65210
G+C content 0.57247
Mean single sequence MFE -47.60
Consensus MFE -11.96
Energy contribution -12.31
Covariance contribution 0.35
Combinations/Pair 1.33
Mean z-score -2.80
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.64
SVM RNA-class probability 0.957106
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 183161 109 + 2517507
---------ACGGGCUAAAAACCCAUUACCGCAACUUGGUCAUCCUGGGGCCCGGGAUGACCCUAACCGUAAGGGGCUGAGCGGGGCCAUAACGAAGUGGUAUCUUCGUUACCUUCAG
---------..(((.......)))....((((.....(((((((((((...)))))))))))....((....))......))))((...((((((((......))))))))))..... ( -43.50, z-score =  -1.99, R)
>droGri2.scaffold_14822 128551 118 - 1097346
GCGCCCAAAGAGGAAGGGAGAGCUCCUGCCACCAAGGGGUCAACCCGGUGGGCUGGAUGACCCGAACCGGAGAAAUCUCUGCGGUUCAAGGGUCAAGUGGUACCUCCGGUACCUCCAG
..((((.....((..((((....)))).))(((..(((.....))))))))))((((((((((((((((.(((....))).))))))..))))))...((((((...)))))))))). ( -55.60, z-score =  -2.65, R)
>droVir3.scaffold_12823 181967 115 - 2474545
GCGUCAGAAACGCGAACCGAAUAUAACGUCACC---GGGACAACCCGGUGGCAAGGGUGAUCCAAACAGAAGAAACCUGAGCGGAUCGCGCACCAAAUGGUAUGUGCGCUACCUCAAA
((((.....))))..............((((((---(((....)))))))))..(((((((((...(((.......)))...)))))((((((..........)))))).)))).... ( -43.70, z-score =  -3.76, R)
>consensus
GCG_C__AAACGGGAAAAAAACCUAAUGCCACCA__GGGUCAACCCGGUGGCCAGGAUGACCCAAACCGAAGAAACCUGAGCGGAUCAAGAACCAAGUGGUAUCUCCGCUACCUCCAG
...........(((............((((((....((((((.((.(.....).)).))))))...(((............)))............))))))..)))........... (-11.96 = -12.31 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 183,161 – 183,270
Length 109
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 55.08
Shannon entropy 0.65210
G+C content 0.57247
Mean single sequence MFE -46.10
Consensus MFE -12.99
Energy contribution -13.23
Covariance contribution 0.25
Combinations/Pair 1.59
Mean z-score -2.31
Structure conservation index 0.28
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.889791
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 183161 109 - 2517507
CUGAAGGUAACGAAGAUACCACUUCGUUAUGGCCCCGCUCAGCCCCUUACGGUUAGGGUCAUCCCGGGCCCCAGGAUGACCAAGUUGCGGUAAUGGGUUUUUAGCCCGU---------
......(((((((((......)))))))))((....(((.(((((.((((.((...((((((((.((...)).)))))))).....)).)))).)))))...)))))..--------- ( -41.40, z-score =  -1.78, R)
>droGri2.scaffold_14822 128551 118 + 1097346
CUGGAGGUACCGGAGGUACCACUUGACCCUUGAACCGCAGAGAUUUCUCCGGUUCGGGUCAUCCAGCCCACCGGGUUGACCCCUUGGUGGCAGGAGCUCUCCCUUCCUCUUUGGGCGC
.((((((((((...))))))...((((((..((((((..(((....)))))))))))))))))))((((((((((....)))...)))((.(((.......))).)).....)))).. ( -52.00, z-score =  -1.87, R)
>droVir3.scaffold_12823 181967 115 + 2474545
UUUGAGGUAGCGCACAUACCAUUUGGUGCGCGAUCCGCUCAGGUUUCUUCUGUUUGGAUCACCCUUGCCACCGGGUUGUCCC---GGUGACGUUAUAUUCGGUUCGCGUUUCUGACGC
...((((..((((((..........))))))((((((..((((.....))))..))))))..))))..(((((((....)))---)))).(((((.(..((.....))..).))))). ( -44.90, z-score =  -3.27, R)
>consensus
CUGGAGGUAACGAAGAUACCACUUGGUCCUCGAACCGCUCAGAUUUCUACGGUUAGGGUCAUCCAGGCCACCGGGUUGACCC__UGGUGGCAAUAGAUUUCCAUCCCGUUU__G_CGC
.....((...(((.(((........))).)))..))...(((((((..(((....(((((((((........))).)))))).....)))....)))))))................. (-12.99 = -13.23 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 183,190 – 183,310
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 63.89
Shannon entropy 0.52508
G+C content 0.57222
Mean single sequence MFE -48.30
Consensus MFE -14.68
Energy contribution -14.13
Covariance contribution -0.54
Combinations/Pair 1.35
Mean z-score -2.32
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.631283
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 183190 120 + 2517507
GUCAUCCUGGGGCCCGGGAUGACCCUAACCGUAAGGGGCUGAGCGGGGCCAUAACGAAGUGGUAUCUUCGUUACCUUCAGCAGGGCAAGUCACCCGCAGAAGCUUUGUCUCUGGCCAAGA
((((((((((...)))))))))).....((....))(((((((((((((..((((((((......))))))))..(((.((.(((.......))))).))))))))).))).)))).... ( -50.60, z-score =  -1.95, R)
>droGri2.scaffold_14822 128589 120 - 1097346
GUCAACCCGGUGGGCUGGAUGACCCGAACCGGAGAAAUCUCUGCGGUUCAAGGGUCAAGUGGUACCUCCGGUACCUCCAGCAGGGACUCAACCCCGAUGAAGCCCUGAAAAAGGCCAAAG
........(((..((((((((((((((((((.(((....))).))))))..))))))...((((((...))))))))))))((((..(((.......)))..)))).......))).... ( -52.40, z-score =  -3.42, R)
>droVir3.scaffold_12823 182002 120 - 2474545
GACAACCCGGUGGCAAGGGUGAUCCAAACAGAAGAAACCUGAGCGGAUCGCGCACCAAAUGGUAUGUGCGCUACCUCAAAAAGGGAUUUCAUCCCGAUGAAGCCUUGCGCAUGGCCAGGG
.....(((((((((..(.(((((((...(((.......)))...))))))).)(((....)))......))))))(((....(((((...)))))..))).(((........)))..))) ( -41.90, z-score =  -1.61, R)
>consensus
GUCAACCCGGUGGCCAGGAUGACCCAAACCGAAGAAACCUGAGCGGAUCAAGAACCAAGUGGUAUCUCCGCUACCUCCAGCAGGGAAUCAAACCCGAUGAAGCCUUGAAAAUGGCCAAGG
.....(((..(((((.((.....))......(((....)))....)))))..........((((.......)))).......)))................(((........)))..... (-14.68 = -14.13 +  -0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 183,190 – 183,310
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 63.89
Shannon entropy 0.52508
G+C content 0.57222
Mean single sequence MFE -49.47
Consensus MFE -20.75
Energy contribution -17.33
Covariance contribution -3.42
Combinations/Pair 1.71
Mean z-score -2.61
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.13
SVM RNA-class probability 0.983240
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 183190 120 - 2517507
UCUUGGCCAGAGACAAAGCUUCUGCGGGUGACUUGCCCUGCUGAAGGUAACGAAGAUACCACUUCGUUAUGGCCCCGCUCAGCCCCUUACGGUUAGGGUCAUCCCGGGCCCCAGGAUGAC
((((((............((((.((((((.....)))).)).))))(((((((((......)))))))))(((((.....((((......)))).(((....)))))))))))))).... ( -46.30, z-score =  -1.80, R)
>droGri2.scaffold_14822 128589 120 + 1097346
CUUUGGCCUUUUUCAGGGCUUCAUCGGGGUUGAGUCCCUGCUGGAGGUACCGGAGGUACCACUUGACCCUUGAACCGCAGAGAUUUCUCCGGUUCGGGUCAUCCAGCCCACCGGGUUGAC
..(..((((.....((((.((((.......)))).))))((((((((((((...))))))...((((((..((((((..(((....))))))))))))))))))))).....))))..). ( -53.50, z-score =  -2.74, R)
>droVir3.scaffold_12823 182002 120 + 2474545
CCCUGGCCAUGCGCAAGGCUUCAUCGGGAUGAAAUCCCUUUUUGAGGUAGCGCACAUACCAUUUGGUGCGCGAUCCGCUCAGGUUUCUUCUGUUUGGAUCACCCUUGCCACCGGGUUGUC
.(((((...((.(((((((((((..(((((...)))))....)))))..((((((..........))))))((((((..((((.....))))..))))))..)))))))))))))..... ( -48.60, z-score =  -3.30, R)
>consensus
CCUUGGCCAUACACAAGGCUUCAUCGGGAUAAAAUCCCUGCUGGAGGUAACGAAGAUACCACUUGGUCCUCGAACCGCUCAGAUUUCUACGGUUAGGGUCAUCCAGGCCACCGGGUUGAC
.(((((...........((......((((.....)))).......((...(((.(((........))).)))..))))...(((((.........)))))..........)))))..... (-20.75 = -17.33 +  -3.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:47:33 2011