Locus 4165

Sequence ID 2L_DroMel_CAF1
Location 11,964,159 – 11,964,384
Length 225
Max. P 0.997886
window6577 window6578 window6579 window6580

overview

Window 7

Location 11,964,159 – 11,964,253
Length 94
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 92.41
Mean single sequence MFE -23.49
Consensus MFE -19.44
Energy contribution -19.92
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -1.77
Structure conservation index 0.83
SVM decision value 1.15
SVM RNA-class probability 0.923078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11964159 94 - 22407834
GAUCUCGUAGAUAAAAGUGGCUUAAACUAUGUAAGCCAUCAACGUUUUAUGAGAGUGGUAUAAACAA--CAGAUACGACUUAGAACGCUCUGGUGA
..(((((((((.....((((((((.......))))))))......)))))))))((.((((......--...)))).))......(((....))). ( -23.70)
>DroSec_CAF1 183584 94 - 1
GAUCUCGUAGAUAAAAGUGGCUUAAACUAUGUAAGCCAUCAACGUUUUAUGAGAGUCUUAUAAAGCA--CAGAUACGACUUAGAACGCUCUAGUGA
....(((((.......((((((((.......))))))))....((((((((((...)))))))))).--....))))).......(((....))). ( -22.80)
>DroSim_CAF1 149961 94 - 1
GAUCUCGUAGAUAAAAGUGGCUUAAACUAUGUAAGCCAUCAACGUUUUAUGAGAGUGGUAUAAAGCA--CAGAUACGACUUAGAACGCUCUGGUGA
..(((((((((.....((((((((.......))))))))......)))))))))((.((((......--...)))).))......(((....))). ( -23.70)
>DroEre_CAF1 158432 94 - 1
GAUCUCGCAGAUAAAAGUGGCUUAAACUAUGUAAGCCAUCAGCGUUUUAUGAGAGUGGCAUAAUGAA--CAGAUACGACUUAGAACGCUCUGGUGA
....(((((((.....((((((((.......))))))))..((((((((.....(((..........--....)))....))))))))))).)))) ( -22.04)
>DroYak_CAF1 154691 96 - 1
GAUCUCGUAGAUAAAGAUGGCUUAAACUAUGUAAGCCAUCAGCGUUUUAUGAGUGUGGUAUAAAGAGCGCAGAUACGACUUAGAAUGCUGUGGUGA
.(((.(.........(((((((((.......)))))))))(((((((((.....((.((((...........)))).)).)))))))))).))).. ( -25.20)
>consensus
GAUCUCGUAGAUAAAAGUGGCUUAAACUAUGUAAGCCAUCAACGUUUUAUGAGAGUGGUAUAAAGAA__CAGAUACGACUUAGAACGCUCUGGUGA
..(((((((((.....((((((((.......))))))))......)))))))))((.((((...........)))).))......(((....))). (-19.44 = -19.92 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,964,253 – 11,964,346
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -28.12
Consensus MFE -22.48
Energy contribution -23.10
Covariance contribution 0.62
Combinations/Pair 1.11
Mean z-score -3.57
Structure conservation index 0.80
SVM decision value 2.95
SVM RNA-class probability 0.997886
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11964253 93 + 22407834
UGCCAUUCCCUGGCCCUCUCCUCGGGCUCAAUAUACAUAUAUAUAUACAUAGAUACAUAGCACAAUAGAUCGAUCUGAUGAGAGGGCCAGCUA
.........(((((((((((.(((((.((.(((((......))))).....(((...((......)).)))))))))).)))))))))))... ( -31.40)
>DroSec_CAF1 183678 89 + 1
UGCCAUUCUCUGGCCCUCUCCUCGGGCUCAAGAUACAUA----UAUACAUAGAUACAUAGUACAAUAGAUCGAUCUGAUGAGAGGGCCAGCUA
.........(((((((((((.(((((.((..(((...((----(.(((.((......)))))..))).)))))))))).)))))))))))... ( -29.70)
>DroSim_CAF1 150055 89 + 1
UGCCAUUCUCUGGCCCUCUCCUCGGGCUCAAGAUACAUA----UAUACAUAGAUACAUAGUACAAUAGAUCGAUCUGUUGAGAGGGCCGGCUA
.........(((((((((((..((((.((..(((...((----(.(((.((......)))))..))).)))))))))..)))))))))))... ( -27.50)
>DroYak_CAF1 154787 89 + 1
UGCCAUUCUCUGGCCCUCUCCUCGGGCUUGAAA-AUGUAUAUACCUCCAUACAUAUUUAGCACAAUAGAUCGAUCU---GAGAGGCCCAGUCU
.........((((.((((((.(((((((.(((.-((((((........)))))).)))))).(....).))))...---)))))).))))... ( -23.90)
>consensus
UGCCAUUCUCUGGCCCUCUCCUCGGGCUCAAGAUACAUA____UAUACAUAGAUACAUAGCACAAUAGAUCGAUCUGAUGAGAGGGCCAGCUA
.........(((((((((((.(((((.((..........................................))))))).)))))))))))... (-22.48 = -23.10 +   0.62)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,964,253 – 11,964,346
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -31.90
Consensus MFE -21.92
Energy contribution -23.05
Covariance contribution 1.13
Combinations/Pair 1.08
Mean z-score -3.41
Structure conservation index 0.69
SVM decision value 2.25
SVM RNA-class probability 0.991178
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11964253 93 - 22407834
UAGCUGGCCCUCUCAUCAGAUCGAUCUAUUGUGCUAUGUAUCUAUGUAUAUAUAUAUGUAUAUUGAGCCCGAGGAGAGGGCCAGGGAAUGGCA
...(((((((((((......(((..((..((((((((((((........))))))).)))))...))..))).)))))))))))......... ( -34.60)
>DroSec_CAF1 183678 89 - 1
UAGCUGGCCCUCUCAUCAGAUCGAUCUAUUGUACUAUGUAUCUAUGUAUA----UAUGUAUCUUGAGCCCGAGGAGAGGGCCAGAGAAUGGCA
...(((((((((((......(((..((...(((((((((((....)))))----)).))))....))..))).)))))))))))......... ( -32.60)
>DroSim_CAF1 150055 89 - 1
UAGCCGGCCCUCUCAACAGAUCGAUCUAUUGUACUAUGUAUCUAUGUAUA----UAUGUAUCUUGAGCCCGAGGAGAGGGCCAGAGAAUGGCA
..((((((((((((......(((..((...(((((((((((....)))))----)).))))....))..))).))))))))).......))). ( -31.11)
>DroYak_CAF1 154787 89 - 1
AGACUGGGCCUCUC---AGAUCGAUCUAUUGUGCUAAAUAUGUAUGGAGGUAUAUACAU-UUUCAAGCCCGAGGAGAGGGCCAGAGAAUGGCA
...((((.((((((---(((....))).(((.(((....(((((((......)))))))-.....))).))).)))))).))))......... ( -29.30)
>consensus
UAGCUGGCCCUCUCAUCAGAUCGAUCUAUUGUACUAUGUAUCUAUGUAUA____UAUGUAUCUUGAGCCCGAGGAGAGGGCCAGAGAAUGGCA
...(((((((((((...(((....))).(((.(((.......((((((......)))))).....))).))).)))))))))))......... (-21.92 = -23.05 +   1.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,964,266 – 11,964,384
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.06
Mean single sequence MFE -28.75
Consensus MFE -19.99
Energy contribution -20.93
Covariance contribution 0.94
Combinations/Pair 1.12
Mean z-score -1.97
Structure conservation index 0.70
SVM decision value 0.55
SVM RNA-class probability 0.776909
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11964266 118 + 22407834
CCCUCUCCUCGGGCUCAAUAUACAUAUAUAUAUACAUAGAUACAUAGCACAAUAGAUCGAUCUGAUGAGAGGGCCAGCUAGGAACAUUCUCUUU--UUUCAAGAGCUUAGUUUUAGCGCA
(((((((.(((((.((.(((((......))))).....(((...((......)).)))))))))).)))))))...(((((((.....(((((.--....))))).....)))))))... ( -31.20)
>DroSec_CAF1 183691 114 + 1
CCCUCUCCUCGGGCUCAAGAUACAUA----UAUACAUAGAUACAUAGUACAAUAGAUCGAUCUGAUGAGAGGGCCAGCUAGGAACAUUCUCUUU--UUUCAAGAGCUUAGUUUUAGCACA
(((((((.(((((.((..(((...((----(.(((.((......)))))..))).)))))))))).)))))))...(((((((.....(((((.--....))))).....)))))))... ( -29.70)
>DroSim_CAF1 150068 114 + 1
CCCUCUCCUCGGGCUCAAGAUACAUA----UAUACAUAGAUACAUAGUACAAUAGAUCGAUCUGUUGAGAGGGCCGGCUAGGAACAUUCUCUUU--UUUCAAGAGCUUAGUUUUAGCGCA
(((((((..((((.((..(((...((----(.(((.((......)))))..))).)))))))))..)))))))...(((((((.....(((((.--....))))).....)))))))... ( -28.00)
>DroYak_CAF1 154800 116 + 1
CCCUCUCCUCGGGCUUGAAA-AUGUAUAUACCUCCAUACAUAUUUAGCACAAUAGAUCGAUCU---GAGAGGCCCAGUCUGGAACAUUCUCUUUUUUUUCAAGAGCUUAGUUUUAGUGCU
.((((((.(((((((.(((.-((((((........)))))).)))))).(....).))))...---))))))...(((((((((((..(((((.......)))))..).))))))).))) ( -26.10)
>consensus
CCCUCUCCUCGGGCUCAAGAUACAUA____UAUACAUAGAUACAUAGCACAAUAGAUCGAUCUGAUGAGAGGGCCAGCUAGGAACAUUCUCUUU__UUUCAAGAGCUUAGUUUUAGCGCA
(((((((.(((((.((..........................................))))))).)))))))...(((((((.....(((((.......))))).....)))))))... (-19.99 = -20.93 +   0.94)

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 11:11:20 2006