Locus 392

Sequence ID 2L_DroMel_CAF1
Location 1,208,836 – 1,209,021
Length 185
Max. P 0.908698
window622 window623 window624

overview

Window 2

Location 1,208,836 – 1,208,945
Length 109
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 84.19
Mean single sequence MFE -25.91
Consensus MFE -15.30
Energy contribution -15.05
Covariance contribution -0.25
Combinations/Pair 1.06
Mean z-score -2.13
Structure conservation index 0.59
SVM decision value 0.16
SVM RNA-class probability 0.611363
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1208836 109 + 22407834
GACAACGCAAAAAGCGCGG----------GCAUAUAAAAUUUUAUAUCUUCCCCAUAACGCGAAUCUCGGGGAAUUACCUGGCAUAUACAUAUAUAUAUAUUGUAUAAUGCCCGACUGC
.....(((.....)))(((----------((((...............((((((..............))))))..........(((((((((....))).)))))))))))))..... ( -26.64)
>DroSim_CAF1 4953 96 + 1
GACAACGCAAAAAGCGCGG----------GCAUAUAAAAUUUUAUAUCUCCACCAUAACGCGAAUCUCGGGGAAUUACCUGGCAUAUAUAUAUA-------------AUGCCCGACUGC
.....(((.....)))(((----------((((((((....)))))....................(((((......)))))............-------------.))))))..... ( -19.30)
>DroEre_CAF1 4285 96 + 1
GACAACGCAAAAAGCGCGG----------GCAUAUAAAAUUUUAUAUCUCCAGCAUAACGCGAAUCCCGGGGAAUUACCUGGCAUACAUAUAAA-------------AUGCCCCGCUGC
............((((.((----------((((.......(((((((.....((.....))(.((.(((((......))))).)).))))))))-------------)))))))))).. ( -26.61)
>DroYak_CAF1 4657 106 + 1
GACAACGCAAAAAGCGCGGGCAGAAGCGGGCAUAUAAAAUUUUAUAUCUGCACCAUAACGCGAAUCCCGGGGAAUUACCUGGCAUAUACAUAUA-------------AUGCCCCGCUGC
............((((.(((((...((((..(((........)))..))))...............(((((......)))))............-------------.))))))))).. ( -31.10)
>consensus
GACAACGCAAAAAGCGCGG__________GCAUAUAAAAUUUUAUAUCUCCACCAUAACGCGAAUCCCGGGGAAUUACCUGGCAUAUACAUAUA_____________AUGCCCCACUGC
......(((.....((((.............((((((....))))))...........))))....(((((......)))))..........................)))........ (-15.30 = -15.05 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,208,905 – 1,209,021
Length 116
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 86.83
Mean single sequence MFE -26.83
Consensus MFE -19.53
Energy contribution -20.10
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -2.20
Structure conservation index 0.73
SVM decision value 0.90
SVM RNA-class probability 0.878479
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1208905 116 + 22407834
UGGCAUAUACAUAUAUAUAUAUUGUAUAAUGCCCGACUGCCGAAA---AAGGCAAACAAGCGGAAUCGGGCCUACAUUUUAAUGAAAUAUGUUUAAAGUGCAGUGCCAGCUCGUAAAUA
.(((((((((((((....))).))))).)))))....((((....---..)))).....((((.....(((((.((((((((..........)))))))).)).)))...))))..... ( -29.40)
>DroSim_CAF1 5022 104 + 1
UGGCAUAUAUAUAUA-------------AUGCCCGACUGCCGAAAA--AAGGCAAACAACCGGAAUCGGGCCUACAUUUUAAUGAAAUAUGUUUAAAGUGCAGUGCCAGCUCGUAAAUA
((((((.........-------------..((((((.((((.....--..))))..(....)...))))))...((((((((..........))))))))..))))))........... ( -26.60)
>DroEre_CAF1 4354 102 + 1
UGGCAUACAUAUAAA-------------AUGCCCCGCUGCCGAAA----AAGCCAACAACCGGAAUCGGGCCUACAUUUUAAUGAAAUAUGUUUGAAGUGCAGUGGCAGCUCGUAAAUA
.(((((.........-------------)))))..(((((((...----..........(((....)))..((.((((((((..........)))))))).)))))))))......... ( -25.70)
>DroYak_CAF1 4736 106 + 1
UGGCAUAUACAUAUA-------------AUGCCCCGCUGCCGAAAAAAAAAGCCAACAACCGGAAUCGGGCCUACAUUUUAAUGAAAUAUGUUUAAAGUGCAGUGGCAGCUCGUAAAUA
.(((((.........-------------)))))..(((((((.................(((....)))..((.((((((((..........)))))))).)))))))))......... ( -25.60)
>consensus
UGGCAUAUACAUAUA_____________AUGCCCCACUGCCGAAA___AAAGCAAACAACCGGAAUCGGGCCUACAUUUUAAUGAAAUAUGUUUAAAGUGCAGUGCCAGCUCGUAAAUA
((((((........................((((((...(((..................)))..))))))...((((((((..........))))))))..))))))........... (-19.53 = -20.10 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,208,905 – 1,209,021
Length 116
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 86.83
Mean single sequence MFE -29.54
Consensus MFE -20.54
Energy contribution -22.54
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.70
SVM decision value 1.06
SVM RNA-class probability 0.908698
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1208905 116 - 22407834
UAUUUACGAGCUGGCACUGCACUUUAAACAUAUUUCAUUAAAAUGUAGGCCCGAUUCCGCUUGUUUGCCUU---UUUCGGCAGUCGGGCAUUAUACAAUAUAUAUAUAUGUAUAUGCCA
.....((((((.(((.(((((.(((((..........))))).)))))))).(....)))))))(((((..---....)))))...(((((.(((((.(((....))))))))))))). ( -31.90)
>DroSim_CAF1 5022 104 - 1
UAUUUACGAGCUGGCACUGCACUUUAAACAUAUUUCAUUAAAAUGUAGGCCCGAUUCCGGUUGUUUGCCUU--UUUUCGGCAGUCGGGCAU-------------UAUAUAUAUAUGCCA
............(((((((((.(((((..........))))).)))))((((((((((((..(........--)..)))).))))))))..-------------..........)))). ( -30.80)
>DroEre_CAF1 4354 102 - 1
UAUUUACGAGCUGCCACUGCACUUCAAACAUAUUUCAUUAAAAUGUAGGCCCGAUUCCGGUUGUUGGCUU----UUUCGGCAGCGGGGCAU-------------UUUAUAUGUAUGCCA
.........((((((.(((((......................)))))(((((((....))))..)))..----....))))))..(((((-------------.........))))). ( -26.05)
>DroYak_CAF1 4736 106 - 1
UAUUUACGAGCUGCCACUGCACUUUAAACAUAUUUCAUUAAAAUGUAGGCCCGAUUCCGGUUGUUGGCUUUUUUUUUCGGCAGCGGGGCAU-------------UAUAUGUAUAUGCCA
.........((((((.(((((.(((((..........))))).)))))(((((((....))))..)))..........))))))..(((((-------------.........))))). ( -29.40)
>consensus
UAUUUACGAGCUGCCACUGCACUUUAAACAUAUUUCAUUAAAAUGUAGGCCCGAUUCCGGUUGUUGGCCUU___UUUCGGCAGCCGGGCAU_____________UAUAUAUAUAUGCCA
............(((((((((.(((((..........))))).)))))((((((((((((................)))).)))))))).........................)))). (-20.54 = -22.54 +   2.00)

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 Mon Dec 4 09:34:50 2006