Locus 3495

Sequence ID X_DroMel_CAF1
Location 9,387,430 – 9,387,584
Length 154
Max. P 0.982173
window5711 window5712 window5713 window5714

overview

Window 1

Location 9,387,430 – 9,387,550
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.78
Mean single sequence MFE -40.97
Consensus MFE -26.50
Energy contribution -26.07
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -3.49
Structure conservation index 0.65
SVM decision value 1.91
SVM RNA-class probability 0.982173
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9387430 120 + 22224390
GGUAAAUAAUACGGCAGAUAUCCGCUAGCCUUGAUAUGUUCAAUGUCCACGAGGCGUAUGCUUGAUGUGUAGUAACUUUGAGCAAUAGUAGCGAGCAUCAAGCAUACGCCGCAUUGGCCC
(((...((((.((((............((((((((((.....)))))...)))))(((((((((((((...((.(((.........))).))..))))))))))))))))).))))))). ( -44.80)
>DroSim_CAF1 4511 118 + 1
AGUAGCUAAUACG-CUGAUAUCCGCUAACCUUGAUAUGUU-AAUGUCCACGAGGCGUAUGCUUGAUAUGUAGUAACUUCAAGUAGUAGUAGCGAGCAUCAAGCAUACGCCGCAUUGGCCC
..((((......)-)))......(((((....(((((...-.)))))...(.(((((((((((((..(((.((.(((.(.....).))).))..)))))))))))))))).).))))).. ( -37.40)
>DroYak_CAF1 4907 120 + 1
GUUAAGUAAUACUGCAGAUACCCGCUACUCCUGAUACAUUUAAUGUACACGCGGCGUAUGCUUGAUAUGUGGUACAUACAAGUACUAGCAGUAAGCAUCAAGUAUACGCCGCAUUGGCCC
.....(((....)))........((((....((.(((((...))))))).((((((((((((((((...((((((......))))))((.....))))))))))))))))))..)))).. ( -40.70)
>consensus
GGUAAAUAAUACGGCAGAUAUCCGCUAACCUUGAUAUGUU_AAUGUCCACGAGGCGUAUGCUUGAUAUGUAGUAACUUCAAGUAAUAGUAGCGAGCAUCAAGCAUACGCCGCAUUGGCCC
.......................((((.....(((((.....))))).....((((((((((((((((...(......)..)))...((.....)).)))))))))))))....)))).. (-26.50 = -26.07 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,387,430 – 9,387,550
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -39.02
Consensus MFE -26.90
Energy contribution -26.36
Covariance contribution -0.55
Combinations/Pair 1.18
Mean z-score -2.97
Structure conservation index 0.69
SVM decision value 1.70
SVM RNA-class probability 0.972902
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9387430 120 - 22224390
GGGCCAAUGCGGCGUAUGCUUGAUGCUCGCUACUAUUGCUCAAAGUUACUACACAUCAAGCAUACGCCUCGUGGACAUUGAACAUAUCAAGGCUAGCGGAUAUCUGCCGUAUUAUUUACC
.((((.(((.(((((((((((((((...((.......)).....((....)).))))))))))))))).))).....((((.....)))))))).((((....)))).(((.....))). ( -41.70)
>DroSim_CAF1 4511 118 - 1
GGGCCAAUGCGGCGUAUGCUUGAUGCUCGCUACUACUACUUGAAGUUACUACAUAUCAAGCAUACGCCUCGUGGACAUU-AACAUAUCAAGGUUAGCGGAUAUCAG-CGUAUUAGCUACU
.(((.((((((((((((((((((((......(((.(.....).))).......)))))))))))))))((((.(((...-...........))).)))).......-.))))).)))... ( -36.96)
>DroYak_CAF1 4907 120 - 1
GGGCCAAUGCGGCGUAUACUUGAUGCUUACUGCUAGUACUUGUAUGUACCACAUAUCAAGCAUACGCCGCGUGUACAUUAAAUGUAUCAGGAGUAGCGGGUAUCUGCAGUAUUACUUAAC
...((.(((((((((((.((((((((.....))..((((......)))).....)))))).)))))))))))((((((...))))))..))....((((....))))............. ( -38.40)
>consensus
GGGCCAAUGCGGCGUAUGCUUGAUGCUCGCUACUACUACUUGAAGUUACUACAUAUCAAGCAUACGCCUCGUGGACAUU_AACAUAUCAAGGCUAGCGGAUAUCUGCCGUAUUACUUACC
.....((((((((((((((((((((.........(((......))).......)))))))))))))))...............(((((..........))))).....)))))....... (-26.90 = -26.36 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,387,470 – 9,387,584
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.90
Mean single sequence MFE -39.87
Consensus MFE -29.41
Energy contribution -28.53
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -3.15
Structure conservation index 0.74
SVM decision value 1.77
SVM RNA-class probability 0.976298
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9387470 114 + 22224390
CAAUGUCCACGAGGCGUAUGCUUGAUGUGUAGUAACUUUGAGCAAUAGUAGCGAGCAUCAAGCAUACGCCGCAUUGGCCCGCCGAGACUUAAAACAUUGUGC--AAUUUCCCCC----GC
((((((......((((((((((((((((...((.(((.........))).))..))))))))))))))))(..((((....))))..).....))))))...--..........----.. ( -41.00)
>DroSim_CAF1 4550 113 + 1
-AAUGUCCACGAGGCGUAUGCUUGAUAUGUAGUAACUUCAAGUAGUAGUAGCGAGCAUCAAGCAUACGCCGCAUUGGCCCGCCGAGACUUAAAACAUUGUGC--AAUUUCCCCC----AC
-......((((((((((((((((((..(((.((.(((.(.....).))).))..))))))))))))))))(..((((....))))..)........))))).--..........----.. ( -34.90)
>DroYak_CAF1 4947 119 + 1
UAAUGUACACGCGGCGUAUGCUUGAUAUGUGGUACAUACAAGUACUAGCAGUAAGCAUCAAGUAUACGCCGCAUUGGCCCGCCGAGAGUUA-AACAUUGUGCCCCACUUCCCCCCUGCCC
....(((((.((((((((((((((((...((((((......))))))((.....)))))))))))))))))).((((....))))......-.....))))).................. ( -43.70)
>consensus
_AAUGUCCACGAGGCGUAUGCUUGAUAUGUAGUAACUUCAAGUAAUAGUAGCGAGCAUCAAGCAUACGCCGCAUUGGCCCGCCGAGACUUAAAACAUUGUGC__AAUUUCCCCC____AC
((((((......((((((((((((((((...(......)..)))...((.....)).)))))))))))))...((((....))))........))))))..................... (-29.41 = -28.53 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,387,470 – 9,387,584
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.90
Mean single sequence MFE -39.87
Consensus MFE -29.63
Energy contribution -29.52
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -2.00
Structure conservation index 0.74
SVM decision value 0.43
SVM RNA-class probability 0.732595
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9387470 114 - 22224390
GC----GGGGGAAAUU--GCACAAUGUUUUAAGUCUCGGCGGGCCAAUGCGGCGUAUGCUUGAUGCUCGCUACUAUUGCUCAAAGUUACUACACAUCAAGCAUACGCCUCGUGGACAUUG
((----((......))--)).((((((((........((....)).(((.(((((((((((((((...((.......)).....((....)).))))))))))))))).))))))))))) ( -40.30)
>DroSim_CAF1 4550 113 - 1
GU----GGGGGAAAUU--GCACAAUGUUUUAAGUCUCGGCGGGCCAAUGCGGCGUAUGCUUGAUGCUCGCUACUACUACUUGAAGUUACUACAUAUCAAGCAUACGCCUCGUGGACAUU-
((----.((((.....--((.....))......)))).))(..(((.((.(((((((((((((((......(((.(.....).))).......))))))))))))))).))))).)...- ( -36.72)
>DroYak_CAF1 4947 119 - 1
GGGCAGGGGGGAAGUGGGGCACAAUGUU-UAACUCUCGGCGGGCCAAUGCGGCGUAUACUUGAUGCUUACUGCUAGUACUUGUAUGUACCACAUAUCAAGCAUACGCCGCGUGUACAUUA
.(((.(..((((.((..(((.....)))-..))))))..)..))).(((((((((((.((((((((.....))..((((......)))).....)))))).)))))))))))........ ( -42.60)
>consensus
GC____GGGGGAAAUU__GCACAAUGUUUUAAGUCUCGGCGGGCCAAUGCGGCGUAUGCUUGAUGCUCGCUACUACUACUUGAAGUUACUACAUAUCAAGCAUACGCCUCGUGGACAUU_
........((((......((.....))......))))((....)).(((.(((((((((((((((.........(((......))).......))))))))))))))).)))........ (-29.63 = -29.52 +  -0.11)

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 Mon Dec 4 11:00:43 2006