Locus 12437

Sequence ID dm3.chrXHet
Location 176,676 – 176,806
Length 130
Max. P 0.998509
window17094 window17095 window17096 window17097

overview

Window 4

Location 176,676 – 176,788
Length 112
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 61.19
Shannon entropy 0.63999
G+C content 0.50107
Mean single sequence MFE -35.22
Consensus MFE -16.39
Energy contribution -18.45
Covariance contribution 2.06
Combinations/Pair 1.46
Mean z-score -1.83
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984551
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 176676 112 + 204112
-GUGGUCGAGCUGAGGCGUGCCUCAGCCAACUACAAGAAGCUCAUUGCGAGGGCGAAAAUGGAUGACUGGAAACGCUUCGUGGGAGAUCAUGCCGACGACCCACGGGGGCGCG
-(((((.(.(((((((....)))))))).)))))......(((.....))).(((.............(....).(((((((((...((.....))...))))))))).))). ( -41.90, z-score =  -1.13, R)
>droAna3.scaffold_3813 5898 111 + 11518
GGGAUCAGCUUAGUACUAGGGUUC--AUGAGUACAAGCAUAGGGUUUUGAGAGUAAAAGAAGAUGAGUGGCGCUCUUUCGUAGAACGGUAUAAACGCGAUCCCUGGGGUCGUG
((((((.((((.(((((.......--...)))))))))...(.((((.....((....((((..(((.....))))))).....)).....)))).))))))).......... ( -27.20, z-score =   0.05, R)
>droVir3.scaffold_12401 571 112 + 1125
-AGGAUUGAAUAUAGUCGGUGUAUGAAUGAGUACAAGCAAAUGCUUGUAAAGGUGAAAGAAGAUGAAUGGCGCUCUUUCCUGGAGCGCAAUAAGGAUGACCCCUGGGGUCGUG
-.(.(((((......))))).).........(((((((....)))))))....................(((((((.....))))))).......(((((((...))))))). ( -31.80, z-score =  -1.99, R)
>droGri2.scaffold_15056 32355 112 - 38174
-AGGUUAGCUUACAGGCAGUGUAUGAAAGAGUACAAGCAAAUGCUUGUAAGAGUGAAAGAGAAUGAAUGGCGUUCCUUUUUGGAGCGCAAUAAGGACGACCCCUGGGGUCGUG
-.......((((((((((.(((((......)))))......))))))))))..................(((((((.....))))))).......(((((((...))))))). ( -40.00, z-score =  -4.27, R)
>consensus
_AGGUUAGAUUAGAGGCAGGGUACGAAUGAGUACAAGCAAAUGCUUGUAAGAGUGAAAGAAGAUGAAUGGCGCUCCUUCGUGGAACGCAAUAAGGACGACCCCUGGGGUCGUG
...............................(((((((....))))))).................((((((((((.....))))))))))....(((((((...))))))). (-16.39 = -18.45 +   2.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 176,676 – 176,788
Length 112
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 61.19
Shannon entropy 0.63999
G+C content 0.50107
Mean single sequence MFE -28.08
Consensus MFE -10.57
Energy contribution -12.95
Covariance contribution 2.38
Combinations/Pair 1.30
Mean z-score -2.47
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.46
SVM RNA-class probability 0.991087
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 176676 112 - 204112
CGCGCCCCCGUGGGUCGUCGGCAUGAUCUCCCACGAAGCGUUUCCAGUCAUCCAUUUUCGCCCUCGCAAUGAGCUUCUUGUAGUUGGCUGAGGCACGCCUCAGCUCGACCAC-
.((((...((((((..(((.....)))..))))))..)))).....(((.................((((..((.....)).))))(((((((....)))))))..)))...- ( -36.10, z-score =  -0.95, R)
>droAna3.scaffold_3813 5898 111 - 11518
CACGACCCCAGGGAUCGCGUUUAUACCGUUCUACGAAAGAGCGCCACUCAUCUUCUUUUACUCUCAAAACCCUAUGCUUGUACUCAU--GAACCCUAGUACUAAGCUGAUCCC
..........((((((((((((....((.....))...))))))...............................(((((((((...--.......))))).)))).)))))) ( -23.60, z-score =  -2.48, R)
>droVir3.scaffold_12401 571 112 - 1125
CACGACCCCAGGGGUCAUCCUUAUUGCGCUCCAGGAAAGAGCGCCAUUCAUCUUCUUUCACCUUUACAAGCAUUUGCUUGUACUCAUUCAUACACCGACUAUAUUCAAUCCU-
...(((((...))))).........((((((.......))))))....................(((((((....)))))))..............................- ( -25.50, z-score =  -3.24, R)
>droGri2.scaffold_15056 32355 112 + 38174
CACGACCCCAGGGGUCGUCCUUAUUGCGCUCCAAAAAGGAACGCCAUUCAUUCUCUUUCACUCUUACAAGCAUUUGCUUGUACUCUUUCAUACACUGCCUGUAAGCUAACCU-
.(((((((...))))))).(((((.(((.(((.....))).)))....................(((((((....)))))))..................))))).......- ( -27.10, z-score =  -3.20, R)
>consensus
CACGACCCCAGGGGUCGUCCUUAUUGCGCUCCACGAAAGAGCGCCAUUCAUCCUCUUUCACCCUCACAAGCAUUUGCUUGUACUCAUUCAAACACCGCCUCUAAGCUAACCC_
.(((((((...))))))).......(((((((.....))))))).....................((((((....))))))................................ (-10.57 = -12.95 +   2.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 176,690 – 176,806
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 65.20
Shannon entropy 0.56846
G+C content 0.47699
Mean single sequence MFE -36.12
Consensus MFE -17.83
Energy contribution -19.82
Covariance contribution 2.00
Combinations/Pair 1.48
Mean z-score -2.82
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.38
SVM RNA-class probability 0.998509
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 176690 116 + 204112
GCGUGCCUCAGCCAACUACAAGAAGCUCAUUGCGAGGGCGAAAAUGGAUGACUGGAAACGCUUCGUGGGAGAUCAUGCCGACGACCCACGGGGGCGCGUCUACAAGAUUUGCCGAG
(((((((((............(((((...((((....))))............(....))))))(((((...((.....))...))))).)))))))))................. ( -36.10, z-score =  -0.01, R)
>droAna3.scaffold_3813 5915 112 + 11518
---AGGGUUCAUGAG-UACAAGCAUAGGGUUUUGAGAGUAAAAGAAGAUGAGUGGCGCUCUUUCGUAGAACGGUAUAAACGCGAUCCCUGGGGUCGUGUUUACAAAAUUCUGCGGG
---.........(((-(.((..(((....((((........))))..)))..))..))))..((((((((.....((((((((((((...)))))))))))).....)))))))). ( -32.90, z-score =  -1.89, R)
>droVir3.scaffold_12401 589 112 + 1125
---UGUAUGAAUGAG-UACAAGCAAAUGCUUGUAAAGGUGAAAGAAGAUGAAUGGCGCUCUUUCCUGGAGCGCAAUAAGGAUGACCCCUGGGGUCGUGUUUAUAAAAUAGUUCGAG
---............-(((((((....)))))))..............(((((.(((((((.....))))))).(((((.(((((((...))))))).)))))......))))).. ( -37.10, z-score =  -4.25, R)
>droGri2.scaffold_15056 32373 112 - 38174
---UGUAUGAAAGAG-UACAAGCAAAUGCUUGUAAGAGUGAAAGAGAAUGAAUGGCGUUCCUUUUUGGAGCGCAAUAAGGACGACCCCUGGGGUCGUGCUUAUAAAGUUGUGAGAG
---............-(((((((....)))))))....................(((((((.....))))))).(((((.(((((((...))))))).)))))............. ( -38.40, z-score =  -5.11, R)
>consensus
___UGUAUGAAUGAG_UACAAGCAAAUGCUUGUAAGAGUGAAAGAAGAUGAAUGGCGCUCCUUCGUGGAACGCAAUAAGGACGACCCCUGGGGUCGUGUUUACAAAAUUGUGCGAG
................(((((((....)))))))..................(((((((((.....)))))))))((((.(((((((...))))))).)))).............. (-17.83 = -19.82 +   2.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 176,690 – 176,806
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 65.20
Shannon entropy 0.56846
G+C content 0.47699
Mean single sequence MFE -27.65
Consensus MFE -12.35
Energy contribution -15.35
Covariance contribution 3.00
Combinations/Pair 1.32
Mean z-score -2.69
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.89
SVM RNA-class probability 0.996149
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 176690 116 - 204112
CUCGGCAAAUCUUGUAGACGCGCCCCCGUGGGUCGUCGGCAUGAUCUCCCACGAAGCGUUUCCAGUCAUCCAUUUUCGCCCUCGCAAUGAGCUUCUUGUAGUUGGCUGAGGCACGC
((((((.....(((.((((((.....((((((..(((.....)))..))))))..)))))).)))...................((((..((.....)).))))))))))...... ( -32.70, z-score =   0.58, R)
>droAna3.scaffold_3813 5915 112 - 11518
CCCGCAGAAUUUUGUAAACACGACCCCAGGGAUCGCGUUUAUACCGUUCUACGAAAGAGCGCCACUCAUCUUCUUUUACUCUCAAAACCCUAUGCUUGUA-CUCAUGAACCCU---
..((((((((..(((((((.(((((....)).))).)))))))..))))).(....).))).......................................-............--- ( -21.70, z-score =  -1.94, R)
>droVir3.scaffold_12401 589 112 - 1125
CUCGAACUAUUUUAUAAACACGACCCCAGGGGUCAUCCUUAUUGCGCUCCAGGAAAGAGCGCCAUUCAUCUUCUUUCACCUUUACAAGCAUUUGCUUGUA-CUCAUUCAUACA---
...(((...............(((((...))))).........((((((.......))))))..)))...............(((((((....)))))))-............--- ( -26.50, z-score =  -3.66, R)
>droGri2.scaffold_15056 32373 112 + 38174
CUCUCACAACUUUAUAAGCACGACCCCAGGGGUCGUCCUUAUUGCGCUCCAAAAAGGAACGCCAUUCAUUCUCUUUCACUCUUACAAGCAUUUGCUUGUA-CUCUUUCAUACA---
.............(((((.(((((((...))))))).))))).(((.(((.....))).)))....................(((((((....)))))))-............--- ( -29.70, z-score =  -5.74, R)
>consensus
CUCGCACAAUUUUAUAAACACGACCCCAGGGGUCGUCCUUAUUGCGCUCCACGAAAGAGCGCCAUUCAUCCUCUUUCACCCUCACAAGCAUUUGCUUGUA_CUCAUUCAUACA___
.............(((((.(((((((...))))))).))))).(((((((.....))))))).....................((((((....))))))................. (-12.35 = -15.35 +   3.00)

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 01:02:13 2011