Locus 3287

Sequence ID 3R_DroMel_CAF1
Location 8,784,337 – 8,784,468
Length 131
Max. P 0.946268
window5301 window5302 window5303

overview

Window 1

Location 8,784,337 – 8,784,428
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 88.07
Mean single sequence MFE -25.55
Consensus MFE -21.56
Energy contribution -21.50
Covariance contribution -0.06
Combinations/Pair 1.16
Mean z-score -1.84
Structure conservation index 0.84
SVM decision value 0.84
SVM RNA-class probability 0.862844
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8784337 91 + 27905053
CCGGCAACAUCAUUUGCUGCCUGCAUUAGUGGCAAAAAUGUGAAUUCAAUCCCAGUGAAUUGUUGCCUUUAAUGCGAUUAAAAGUGACAGA
..((((.((.....)).))))((((((((.(((((.......((((((.......)))))).))))).))))))))............... ( -22.80)
>DroSim_CAF1 222790 91 + 1
CCGGCAACAUCAUUUGCUGCCUGCAUUACUGGCCUAAAUGUGAAUUCCAUCCCGGGGAAUUGUUGCCUUUAAUGCAAUAAAAAUUGGCAAA
((((((.((.....)).))))(((((((..(((...(((...((((((.......))))))))))))..))))))).........)).... ( -23.20)
>DroEre_CAF1 222873 90 + 1
CCGGCAACAUCAUUUGCUGGCUGCAUUAGUGGCAGGAAUGUGAAUUCAAUCC-GGUGAAUUGUUGCCUUUAAUGCGAUUAAGGGGGGCAGA
(((((((......)))))))((((.(((((.((((((.((......)).)))-((..(....)..)).....))).))))).....)))). ( -29.00)
>DroYak_CAF1 216194 90 + 1
CCGGCAACAUAAUUUGCUGGCUGCAUUAGUGGCAGAAAUGUGAAUUCAAUCC-UGUGAAUUGCUGCCUUUAAUGCGAUUAAGAGGGGCAGA
(((((((......)))))))((((.....(.(((....))).)......(((-(.(.((((((..........)))))).).)))))))). ( -27.20)
>consensus
CCGGCAACAUCAUUUGCUGCCUGCAUUAGUGGCAGAAAUGUGAAUUCAAUCC_GGUGAAUUGUUGCCUUUAAUGCGAUUAAAAGGGGCAGA
.((((((......))))))..((((((((.(((((.......((((((.......)))))).))))).))))))))............... (-21.56 = -21.50 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,784,337 – 8,784,428
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 88.07
Mean single sequence MFE -23.28
Consensus MFE -20.76
Energy contribution -21.95
Covariance contribution 1.19
Combinations/Pair 1.08
Mean z-score -2.01
Structure conservation index 0.89
SVM decision value 1.36
SVM RNA-class probability 0.946268
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8784337 91 - 27905053
UCUGUCACUUUUAAUCGCAUUAAAGGCAACAAUUCACUGGGAUUGAAUUCACAUUUUUGCCACUAAUGCAGGCAGCAAAUGAUGUUGCCGG
................((((((..(((((((((((....))))))...........)))))..)))))).(((((((.....))))))).. ( -26.40)
>DroSim_CAF1 222790 91 - 1
UUUGCCAAUUUUUAUUGCAUUAAAGGCAACAAUUCCCCGGGAUGGAAUUCACAUUUAGGCCAGUAAUGCAGGCAGCAAAUGAUGUUGCCGG
....((.........(((((((..(((...((((((.......)))))).........)))..)))))))(((((((.....))))))))) ( -27.00)
>DroEre_CAF1 222873 90 - 1
UCUGCCCCCCUUAAUCGCAUUAAAGGCAACAAUUCACC-GGAUUGAAUUCACAUUCCUGCCACUAAUGCAGCCAGCAAAUGAUGUUGCCGG
................((((((..((((..........-(((.((......)).)))))))..))))))..((.((((......)))).)) ( -19.00)
>DroYak_CAF1 216194 90 - 1
UCUGCCCCUCUUAAUCGCAUUAAAGGCAGCAAUUCACA-GGAUUGAAUUCACAUUUCUGCCACUAAUGCAGCCAGCAAAUUAUGUUGCCGG
................((((((..((((((((((....-.)))))...........)))))..))))))..((.((((......)))).)) ( -20.70)
>consensus
UCUGCCACUCUUAAUCGCAUUAAAGGCAACAAUUCACC_GGAUUGAAUUCACAUUUCUGCCACUAAUGCAGCCAGCAAAUGAUGUUGCCGG
....((..........((((((..(((((((((((....))))))...........)))))..)))))).(((((((.....))))))))) (-20.76 = -21.95 +   1.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,784,355 – 8,784,468
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 76.04
Mean single sequence MFE -23.57
Consensus MFE -13.95
Energy contribution -14.83
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.59
SVM decision value 0.07
SVM RNA-class probability 0.566379
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8784355 113 - 27905053
GCUAGGCUACAAUUAUUUGCCAAGUUGGCAAGUUGGCCUUUCUGUCACUUUUAAUCGCAUUAAAGGCAACAAUUCACUGGGAUUGAAUUCACAUUUUUGCCACUAAUGCAGGC
(((((((((.....(((((((.....))))))))))))).................((((((..(((((((((((....))))))...........)))))..)))))).))) ( -31.80)
>DroSim_CAF1 222808 103 - 1
UCGACGAUCCAAUUAGUUGCCAAGU----------ACCUUUUUGCCAAUUUUUAUUGCAUUAAAGGCAACAAUUCCCCGGGAUGGAAUUCACAUUUAGGCCAGUAAUGCAGGC
........((....(((((.((((.----------.....)))).))))).....(((((((..(((...((((((.......)))))).........)))..))))))))). ( -20.30)
>DroEre_CAF1 222891 102 - 1
GCGAGGCUGCAAUUAGUUGCCAACU----------UUCUUUCUGCCCCCCUUAAUCGCAUUAAAGGCAACAAUUCACC-GGAUUGAAUUCACAUUCCUGCCACUAAUGCAGCC
....(((((((.(((((.((.....----------.......((((....(((((...))))).))))..........-(((.((......)).))).)).)))))))))))) ( -25.90)
>DroYak_CAF1 216212 92 - 1
----------AAUUAGUUGUCAACA----------UUCUUUCUGCCCCUCUUAAUCGCAUUAAAGGCAGCAAUUCACA-GGAUUGAAUUCACAUUUCUGCCACUAAUGCAGCC
----------...............----------.....................((((((..((((((((((....-.)))))...........)))))..)))))).... ( -16.30)
>consensus
GCGAGGCU_CAAUUAGUUGCCAACU__________UCCUUUCUGCCACUCUUAAUCGCAUUAAAGGCAACAAUUCACC_GGAUUGAAUUCACAUUUCUGCCACUAAUGCAGCC
........................................................((((((..(((((((((((....))))))...........)))))..)))))).... (-13.95 = -14.83 +   0.88)

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 10:57:31 2006