Locus 12398

Sequence ID dm3.chr4
Location 614,138 – 614,262
Length 124
Max. P 0.999133
window17032 window17033 window17034 window17035

overview

Window 2

Location 614,138 – 614,248
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 60.30
Shannon entropy 0.57133
G+C content 0.49802
Mean single sequence MFE -37.40
Consensus MFE -18.07
Energy contribution -19.20
Covariance contribution 1.13
Combinations/Pair 1.52
Mean z-score -3.05
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.66
SVM RNA-class probability 0.999133
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 614138 110 + 1351857
AACUACAAGAAGCUCAUUGGAAGGGCGAAGAUGGAUGACUGGAAACGCUUCGUGGGAGAUCAUGCCGACGACCCAUGGGGGCGCGUCUACAAGAUUUGCCGAGGCCGCAG
..((.(((........)))..)).(((.............(....)(((((..((.(((((.((..((((.(((....)))..))))..)).))))).)))))))))).. ( -30.50, z-score =   0.59, R)
>droAna3.scaffold_13089 82066 107 - 978470
---UACAAGCAUAGGGUUUUGCGUGUGAAAGAUGAUGAGUGGCGUUCUUUCGUAGAUCGAAAUAAACACGAUCCCUGGGGUCGUGUUUAUAAGAUUCUGCGGGAGAAUGG
---((((.(((........))).))))...............((((((..((((((((...(((((((((((((...)))))))))))))..)).))))))..)))))). ( -42.90, z-score =  -5.76, R)
>droGri2.scaffold_15040 43428 110 - 162499
GAGUACAAGCAAAUGCUUGUAAGAGUGAAAGAGGAUGAAUGGCGUUCCUUUUUGGAGCGCAAUAAGGACGACCCCUGGGGUCGUGCUUAUAAAGUUGUGAGAGGUAGGCG
...(((((((....)))))))...((...............(((((((.....))))))).(((((.(((((((...))))))).))))).................)). ( -38.80, z-score =  -3.98, R)
>consensus
_A_UACAAGCAAAUGAUUGUAAGAGUGAAAGAGGAUGAAUGGCGUUCCUUCGUGGAACGAAAUAAAGACGACCCCUGGGGUCGUGUUUAUAAGAUUCUGCGAGGCAGCAG
............................................(((((((((((((....(((((.(((((((...))))))).)))))....)))))))))))))... (-18.07 = -19.20 +   1.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 614,138 – 614,248
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 60.30
Shannon entropy 0.57133
G+C content 0.49802
Mean single sequence MFE -27.14
Consensus MFE -8.79
Energy contribution -10.35
Covariance contribution 1.56
Combinations/Pair 1.28
Mean z-score -2.80
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.970658
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 614138 110 - 1351857
CUGCGGCCUCGGCAAAUCUUGUAGACGCGCCCCCAUGGGUCGUCGGCAUGAUCUCCCACGAAGCGUUUCCAGUCAUCCAUCUUCGCCCUUCCAAUGAGCUUCUUGUAGUU
((((((....((...(((.(((.((((.((((....)))))))).))).)))...))..(((((.................................))))))))))).. ( -25.81, z-score =   0.77, R)
>droAna3.scaffold_13089 82066 107 + 978470
CCAUUCUCCCGCAGAAUCUUAUAAACACGACCCCAGGGAUCGUGUUUAUUUCGAUCUACGAAAGAACGCCACUCAUCAUCUUUCACACGCAAAACCCUAUGCUUGUA---
...((((..((.(((.((..((((((((((((....)).))))))))))...))))).))..))))..................(((.(((........))).))).--- ( -25.90, z-score =  -4.23, R)
>droGri2.scaffold_15040 43428 110 + 162499
CGCCUACCUCUCACAACUUUAUAAGCACGACCCCAGGGGUCGUCCUUAUUGCGCUCCAAAAAGGAACGCCAUUCAUCCUCUUUCACUCUUACAAGCAUUUGCUUGUACUC
....................(((((.(((((((...))))))).))))).(((.(((.....))).)))....................(((((((....)))))))... ( -29.70, z-score =  -4.94, R)
>consensus
CCACUACCUCGCAAAAUCUUAUAAACACGACCCCAGGGGUCGUCCUUAUUACGAUCCACGAAGGAACGCCACUCAUCCUCUUUCACACUUACAACCAUAUGCUUGUA_U_
....................(((((.(((((((...))))))).)))))..........((((((.............)))))).......................... ( -8.79 = -10.35 +   1.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 614,172 – 614,262
Length 90
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 55.67
Shannon entropy 0.62163
G+C content 0.53356
Mean single sequence MFE -33.43
Consensus MFE -18.07
Energy contribution -19.20
Covariance contribution 1.13
Combinations/Pair 1.52
Mean z-score -2.52
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.65
SVM RNA-class probability 0.999110
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 614172 90 + 1351857
AUGACUGGAAACGCUUCGUGGGAGAUCAUGCCGACGACCCAUGGGGGCGCGUCUACAAGAUUUGCCGAGGCCGCAGAAAGUGCACGGAGA------
......(....).((((((((.(((((.((..((((.(((....)))..))))..)).))))).))......(((.....))))))))).------ ( -29.30, z-score =  -0.35, R)
>droAna3.scaffold_13089 82097 96 - 978470
AUGAGUGGCGUUCUUUCGUAGAUCGAAAUAAACACGAUCCCUGGGGUCGUGUUUAUAAGAUUCUGCGGGAGAAUGGGAAGGAGGGGUCCAGGGAUA
........((((((..((((((((...(((((((((((((...)))))))))))))..)).))))))..))))))....(((....)))....... ( -39.60, z-score =  -4.78, R)
>droGri2.scaffold_15040 43462 90 - 162499
AUGAAUGGCGUUCCUUUUUGGAGCGCAAUAAGGACGACCCCUGGGGUCGUGCUUAUAAAGUUGUGAGAGGUAGGCGUAGGGAAGCGGAUG------
.......(((((((.....))))))).(((((.(((((((...))))))).))))).................((........)).....------ ( -31.40, z-score =  -2.43, R)
>consensus
AUGAAUGGCGUUCCUUCGUGGAACGAAAUAAAGACGACCCCUGGGGUCGUGUUUAUAAGAUUCUGCGAGGCAGCAGAAAGGAAGCGGACA______
..........(((((((((((((....(((((.(((((((...))))))).)))))....)))))))))))))....................... (-18.07 = -19.20 +   1.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 614,172 – 614,262
Length 90
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 55.67
Shannon entropy 0.62163
G+C content 0.53356
Mean single sequence MFE -22.77
Consensus MFE -8.60
Energy contribution -9.50
Covariance contribution 0.90
Combinations/Pair 1.35
Mean z-score -1.95
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.928944
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 614172 90 - 1351857
------UCUCCGUGCACUUUCUGCGGCCUCGGCAAAUCUUGUAGACGCGCCCCCAUGGGUCGUCGGCAUGAUCUCCCACGAAGCGUUUCCAGUCAU
------.....(((.(((....(((.(.(((....(((.(((.((((.((((....)))))))).))).)))......))).))))....)))))) ( -23.20, z-score =   0.57, R)
>droAna3.scaffold_13089 82097 96 + 978470
UAUCCCUGGACCCCUCCUUCCCAUUCUCCCGCAGAAUCUUAUAAACACGACCCCAGGGAUCGUGUUUAUUUCGAUCUACGAAAGAACGCCACUCAU
.......(((....)))......((((..((.(((.((..((((((((((((....)).))))))))))...))))).))..)))).......... ( -23.50, z-score =  -3.38, R)
>droGri2.scaffold_15040 43462 90 + 162499
------CAUCCGCUUCCCUACGCCUACCUCUCACAACUUUAUAAGCACGACCCCAGGGGUCGUCCUUAUUGCGCUCCAAAAAGGAACGCCAUUCAU
------.....((........)).................(((((.(((((((...))))))).))))).(((.(((.....))).)))....... ( -21.60, z-score =  -3.06, R)
>consensus
______UAUCCGCCUCCUUACCACUACCUCGCAAAAUCUUAUAAACACGACCCCAGGGGUCGUCCUUAUUACGAUCCACGAAGGAACGCCACUCAU
.........................((.(((.........(((((.(((((((...))))))).))))).........))).))............ ( -8.60 =  -9.50 +   0.90)

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 01:01:19 2011