Locus 677

Sequence ID 2L_DroMel_CAF1
Location 1,980,709 – 1,980,869
Length 160
Max. P 0.779085
window1107 window1108 window1109

overview

Window 7

Location 1,980,709 – 1,980,829
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.39
Mean single sequence MFE -26.93
Consensus MFE -23.56
Energy contribution -22.88
Covariance contribution -0.69
Combinations/Pair 1.10
Mean z-score -1.66
Structure conservation index 0.88
SVM decision value 0.02
SVM RNA-class probability 0.541306
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1980709 120 + 22407834
AAAAAUACGGAUAAAUGGUUUGCUAUUCCUAAUAAAAUAAAGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCCGCUGCGGUCACACUGCGGCCAGGAGGAAAUAAAGGUAUCAAA
.........((((....((((.(...((((..................(..((((((....))))))..)....((((((.(.(....).).))))))))))).)))).....))))... ( -29.50)
>DroSim_CAF1 6683 120 + 1
AAAAAUACGGAUAAAUGGUUUGCUAUUCCUAAUAAAAUAAAGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCCGCUGCGGUCACACUGCGGCCAGGAGGAAAUAAAGGUAUCAAA
.........((((....((((.(...((((..................(..((((((....))))))..)....((((((.(.(....).).))))))))))).)))).....))))... ( -29.50)
>DroEre_CAF1 6478 120 + 1
AAAAAUACGGAUAAAUGGUUUGCUAUUCCUAAUAAAAUAAAGCAAUAAGAAUAUCGAACUAUCGAUGAGCGAUAGGCUCGUGCGGUCACACUACGGCUAGGAGGAAAUAAAGGUAUCGAA
.........((((....((((.(...((((...........(((........(((((....)))))((((.....)))).)))((((.......))))))))).)))).....))))... ( -23.00)
>DroYak_CAF1 6481 120 + 1
AAAAAUACGGAUAAAUGGUUUGCUAUUCCUAAUAAAAUAAAGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCUCCUGCGGUCACACUACGGCUAGGAGGAAAUAAAGGUAUCGAA
........(((...((((....)))))))........................((((.((((((.....)))))).(((((((.((......)).)).)))))............)))). ( -25.70)
>consensus
AAAAAUACGGAUAAAUGGUUUGCUAUUCCUAAUAAAAUAAAGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCCCCUGCGGUCACACUACGGCCAGGAGGAAAUAAAGGUAUCAAA
.........((((....((((.(...((((...........(((.......((((((....))))))(((.....)))..)))((((.......))))))))).)))).....))))... (-23.56 = -22.88 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,980,749 – 1,980,869
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.86
Mean single sequence MFE -38.60
Consensus MFE -26.44
Energy contribution -27.12
Covariance contribution 0.69
Combinations/Pair 1.18
Mean z-score -3.03
Structure conservation index 0.68
SVM decision value 0.55
SVM RNA-class probability 0.779085
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1980749 120 + 22407834
AGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCCGCUGCGGUCACACUGCGGCCAGGAGGAAAUAAAGGUAUCAAACUAUCGCAGGUGGCAAGGCAGCGAUAGAUCGGAUAGAAAA
.............((((.(((((....(((.....)))(((((.(((((.((((((..((...((.((....)).))...)).)))))))))))...)))))))))).))))........ ( -41.40)
>DroSim_CAF1 6723 120 + 1
AGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCCGCUGCGGUCACACUGCGGCCAGGAGGAAAUAAAGGUAUCAAACUAUCGCAGGUGGCAAGGCAGCGAUAGAUCGGAUGGAAAA
.............((((.(((((....(((.....)))(((((.(((((.((((((..((...((.((....)).))...)).)))))))))))...)))))))))).))))........ ( -41.40)
>DroEre_CAF1 6518 115 + 1
AGCAAUAAGAAUAUCGAACUAUCGAUGAGCGAUAGGCUCGUGCGGUCACACUACGGCUAGGAGGAAAUAAAGGUAUCGAACUAUCGCAGGUGGUAGGCCAGUGAUAUAUCGA-----AUA
...........((((...((((((.....)))))).(((.(((.((......)).)).).)))........))))((((..((((((.(((.....))).))))))..))))-----... ( -28.40)
>DroYak_CAF1 6521 120 + 1
AGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCUCCUGCGGUCACACUACGGCUAGGAGGAAAUAAAGGUAUCGAACUAUCGCAGGUGGUAGGCCUGCGAUAGAUCGGAUGGGAUA
...........((((...((((((.....)))))).(((((((.((......)).)).)))))........))))((((.(((((((((((.....))))))))))).))))........ ( -43.20)
>consensus
AGCAAUAAGAAUAUCGAACUAUCGAUGGGCGAUAGGCCCCUGCGGUCACACUACGGCCAGGAGGAAAUAAAGGUAUCAAACUAUCGCAGGUGGCAAGCCAGCGAUAGAUCGGAUGGAAAA
.............((((.((((((...(((.....)))(((...(((((.((((((.(((...((.((....)).))...))))))))))))))..)))..)))))).))))........ (-26.44 = -27.12 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,980,749 – 1,980,869
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.86
Mean single sequence MFE -31.70
Consensus MFE -22.08
Energy contribution -22.32
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.57
Structure conservation index 0.70
SVM decision value 0.51
SVM RNA-class probability 0.764353
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1980749 120 - 22407834
UUUUCUAUCCGAUCUAUCGCUGCCUUGCCACCUGCGAUAGUUUGAUACCUUUAUUUCCUCCUGGCCGCAGUGUGACCGCAGCGGCCUAUCGCCCAUCGAUAGUUCGAUAUUCUUAUUGCU
.........(((.((((((((((...(.((((((((.(((...((..........))...)))..))))).))).).)))))(((.....)))....))))).))).............. ( -33.00)
>DroSim_CAF1 6723 120 - 1
UUUUCCAUCCGAUCUAUCGCUGCCUUGCCACCUGCGAUAGUUUGAUACCUUUAUUUCCUCCUGGCCGCAGUGUGACCGCAGCGGCCUAUCGCCCAUCGAUAGUUCGAUAUUCUUAUUGCU
.........(((.((((((((((...(.((((((((.(((...((..........))...)))..))))).))).).)))))(((.....)))....))))).))).............. ( -33.00)
>DroEre_CAF1 6518 115 - 1
UAU-----UCGAUAUAUCACUGGCCUACCACCUGCGAUAGUUCGAUACCUUUAUUUCCUCCUAGCCGUAGUGUGACCGCACGAGCCUAUCGCUCAUCGAUAGUUCGAUAUUCUUAUUGCU
...-----((((..((((.(.((.......)).).))))..)))).................(((.(((((((....))))((((.....))))(((((....))))).....))).))) ( -24.70)
>DroYak_CAF1 6521 120 - 1
UAUCCCAUCCGAUCUAUCGCAGGCCUACCACCUGCGAUAGUUCGAUACCUUUAUUUCCUCCUAGCCGUAGUGUGACCGCAGGAGCCUAUCGCCCAUCGAUAGUUCGAUAUUCUUAUUGCU
.........(((.((((((((((.......)))))))))).))).............(((((.((.((......)).))))))).((((((.....))))))..(((((....))))).. ( -36.10)
>consensus
UAUUCCAUCCGAUCUAUCGCUGCCCUACCACCUGCGAUAGUUCGAUACCUUUAUUUCCUCCUAGCCGCAGUGUGACCGCAGCAGCCUAUCGCCCAUCGAUAGUUCGAUAUUCUUAUUGCU
.........(((.((((((.((......((((((((.(((...((..........))...)))..))))).)))........(((.....))))).)))))).))).............. (-22.08 = -22.32 +   0.25)

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 09:42:40 2006