Locus 3273

Sequence ID 3L_DroMel_CAF1
Location 9,601,621 – 9,601,775
Length 154
Max. P 0.941022
window5084 window5085 window5086

overview

Window 4

Location 9,601,621 – 9,601,735
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.89
Mean single sequence MFE -19.52
Consensus MFE -18.12
Energy contribution -18.38
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.93
SVM decision value 1.31
SVM RNA-class probability 0.941022
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9601621 114 + 23771897
CACUCUAAAAAUACAAUAAU------UCCUUACAUAAAAAUUGAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGG
....................------.............((((........))))........(((((((((.(((..((((((((.......)))))))))))......))))))).)) ( -19.60)
>DroSec_CAF1 262 114 + 1
CACUCUAAAAAUACAAUAAU------UCCUUGCAUAAACAUUAAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGG
...............(((((------(...((......))....)))))).............(((((((((.(((..((((((((.......)))))))))))......))))))).)) ( -19.70)
>DroSim_CAF1 264 114 + 1
CACUCUAAAAAUACAAUAAU------UACUUACGUAAACAUUAAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGG
...................(------(((....))))..........................(((((((((.(((..((((((((.......)))))))))))......))))))).)) ( -20.30)
>DroEre_CAF1 306 119 + 1
CACUCUGAAAC-ACAAUACUCGUAUUUCCUUAAAUCAAAAUUGUAAUAAUACAAUAAAACAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAAAGUGAUUUCCAGAGCUAUGG
......((((.-((.......)).))))...........((((((....))))))........(((((((((.(((.((.((((((.......)))))))))))......))))))).)) ( -18.50)
>consensus
CACUCUAAAAAUACAAUAAU______UCCUUACAUAAAAAUUAAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGG
...............................................................(((((((((.(((..((((((((.......)))))))))))......))))))).)) (-18.12 = -18.38 +   0.25)

alignment

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secondary structure

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Window 5

Location 9,601,621 – 9,601,735
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.89
Mean single sequence MFE -27.70
Consensus MFE -22.80
Energy contribution -22.55
Covariance contribution -0.25
Combinations/Pair 1.14
Mean z-score -1.36
Structure conservation index 0.82
SVM decision value -0.05
SVM RNA-class probability 0.506063
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9601621 114 - 23771897
CCAUAGCUCUGGAGAUCACUCUGUACAACGUGAGUGCACAGAAGGUGGAGAGCCAGGUAUAUUAUAUUGUAUAAUUUCAAUUUUUAUGUAAGGA------AUUAUUGUAUUUUUAGAGUG
.....(((((((((((((((((((...((....))..)))))..))))....((...(((((...((((........))))....))))).)).------.........)))))))))). ( -25.60)
>DroSec_CAF1 262 114 - 1
CCAUAGCUCUGGAGAUCACUCUGUACAACGUGAGUGCACAGAAGGUGGAGAGCCAGGUAUAUUAUAUUGUAUAAUUUUAAUGUUUAUGCAAGGA------AUUAUUGUAUUUUUAGAGUG
.....(((((((((((((((((((...((....))..)))))..))))....((..(((((..((((((........)))))).)))))..)).------.........)))))))))). ( -29.60)
>DroSim_CAF1 264 114 - 1
CCAUAGCUCUGGAGAUCACUCUGUACAACGUGAGUGCACAGAAGGUGGAGAGCCAGGUAUAUUAUAUUGUAUAAUUUUAAUGUUUACGUAAGUA------AUUAUUGUAUUUUUAGAGUG
.....(((((((((((.(((((((...((....))..))))).(((.....)))..(((((......)))))......((((.((((....)))------).))))))))))))))))). ( -28.30)
>DroEre_CAF1 306 119 - 1
CCAUAGCUCUGGAAAUCACUUUGUACAACGUGAGUGCACAGAAGGUGGAGAGCCAGGUAUGUUUUAUUGUAUUAUUACAAUUUUGAUUUAAGGAAAUACGAGUAUUGU-GUUUCAGAGUG
.....(((((..((((((.(((((...((....))..))))).(((.....)))...........((((((....))))))..))))))...(((((((((...))))-)))))))))). ( -27.30)
>consensus
CCAUAGCUCUGGAGAUCACUCUGUACAACGUGAGUGCACAGAAGGUGGAGAGCCAGGUAUAUUAUAUUGUAUAAUUUCAAUGUUUAUGUAAGGA______AUUAUUGUAUUUUUAGAGUG
.....(((((((((((.(((((((...((....))..))))).(((.....)))..(((((......)))))..................................))))))))))))). (-22.80 = -22.55 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,601,655 – 9,601,775
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -22.50
Consensus MFE -18.43
Energy contribution -19.48
Covariance contribution 1.06
Combinations/Pair 1.09
Mean z-score -2.10
Structure conservation index 0.82
SVM decision value 0.44
SVM RNA-class probability 0.737395
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9601655 120 + 23771897
UUGAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGGUCACAAAGUAGACCAUAAUCAUGCCCAUCCACACCCAGCC
........................((((((((.(((..((((((((.......)))))))))))......)))))(((((((........)))))))..................))).. ( -26.10)
>DroSec_CAF1 296 120 + 1
UUAAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGGUCACAAAGUAGACCAUAAUCAUGCCCAUCCACACCCAGCC
........................((((((((.(((..((((((((.......)))))))))))......)))))(((((((........)))))))..................))).. ( -26.10)
>DroSim_CAF1 298 120 + 1
UUAAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGGUCACAAAGUAGACCAUAAUCAUGCCCAUCCACACCCAUCC
..........................(((....(((..((((((((.......))))))))))).......((..(((((((........))))))).))..)))............... ( -25.70)
>DroEre_CAF1 345 120 + 1
UUGUAAUAAUACAAUAAAACAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAAAGUGAUUUCCAGAGCUAUGGUCACAAAGUAGACCAUAAUCAUGCCCAUCCACACCCAACC
(((((....)))))............(((....(((.((.((((((.......))))))))))).......((..(((((((........))))))).))..)))............... ( -22.10)
>DroYak_CAF1 297 120 + 1
UUAUAAUAAUACAAUACAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGGUCACAAAGUAAACCAUAAUCAUGCCCAUCCACACCCAGCC
..............(((.....((((((((((.(((..((((((((.......)))))))))))......))))))).)))......))).............................. ( -21.50)
>DroPer_CAF1 280 95 + 1
-------------------------UGGGUCUCCACUUUCUGCGCGCUUACAUUGUACAAGCUGAUCUCCAGAGUUAUUGUCACAAAGUACACCAUAAUCAUGCCCAUCCAUACCCAGCC
-------------------------(((((..................(((.((((((((.(((.....))).....)))).)))).)))..........(((......))))))))... ( -13.50)
>consensus
UUAAAAUUAUACAAUAUAAUAUACCUGGCUCUCCACCUUCUGUGCACUCACGUUGUACAGAGUGAUCUCCAGAGCUAUGGUCACAAAGUAGACCAUAAUCAUGCCCAUCCACACCCAGCC
..........................(((....(((..((((((((.......))))))))))).......((..(((((((........))))))).))..)))............... (-18.43 = -19.48 +   1.06)

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 10:53:32 2006