Locus 1272

Sequence ID 2L_DroMel_CAF1
Location 3,385,236 – 3,385,369
Length 133
Max. P 0.988832
window2078 window2079 window2080

overview

Window 8

Location 3,385,236 – 3,385,337
Length 101
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 78.16
Mean single sequence MFE -22.88
Consensus MFE -9.85
Energy contribution -9.49
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -3.50
Structure conservation index 0.43
SVM decision value 2.14
SVM RNA-class probability 0.988832
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3385236 101 + 22407834
AGUGAGU--GCUGCAAGUCGAAUGGAAUUCG-AUUCGAUUUGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCC
.((((((--((..((((((((((.(....).-)))))))))).....))))))))...............((....((((((.....))))))...))...... ( -29.00)
>DroPse_CAF1 13343 90 + 1
------U--UCUAAAAACUCGAUCAAAC------UCGAUUUGAUUUCGUAUUUAUAUUCAAUUUCUCUUAGAUAUUUGCUGUUCUAUGCAGCAUUUUCUACAUC
------.--..((((.((..(((((((.------....)))))))..)).))))..............((((....((((((.....))))))...)))).... ( -15.60)
>DroEre_CAF1 8052 98 + 1
AGUGAGUAGACUGCAAGUCGAAUAGAAUUC------GAUUUGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCC
.(((((((((...((((((((((...))))------))))))...)).)))))))...............((....((((((.....))))))...))...... ( -24.80)
>DroYak_CAF1 8185 96 + 1
AGUGAGU--GCUGCAAGUCGAAUAGAAUUC------GAUUUGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCC
.((((((--((..((((((((((...))))------)))))).....))))))))...............((....((((((.....))))))...))...... ( -25.30)
>DroAna_CAF1 13686 95 + 1
CCCGAGU--GGAGCA-------UCGAAUUCGAAUUCGAUUUGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCCACGCAGCGUUUUCCACUCC
...((((--((((..-------..((((..((((.(((.......))).))))..))))..................(((((.....)))))...)))))))). ( -27.00)
>DroPer_CAF1 12770 90 + 1
------U--UCUAAAAACUCGAUCAAAC------UCGAUUUGAUUUCGUAUUUAUAUUCAAUUUCUCUUAGAUAUUUGCUGUUCUAUGCAGCAUUUUCUACAUC
------.--..((((.((..(((((((.------....)))))))..)).))))..............((((....((((((.....))))))...)))).... ( -15.60)
>consensus
AGUGAGU__GCUGCAAGUCGAAUCGAAUUC____UCGAUUUGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCC
...............................................(((((((..............))))))).((((((.....))))))........... ( -9.85 =  -9.49 +  -0.36)

alignment

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secondary structure

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Window 9

Location 3,385,236 – 3,385,337
Length 101
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 78.16
Mean single sequence MFE -21.72
Consensus MFE -8.82
Energy contribution -9.10
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -2.91
Structure conservation index 0.41
SVM decision value 1.23
SVM RNA-class probability 0.933711
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3385236 101 - 22407834
GGAGUGGAAAAUGCUGCAUAGAGCAGCAAAUAUCUAGAAUAAAUUGAAUAUAAAUACGAAAUCAAAUCGAAU-CGAAUUCCAUUCGACUUGCAGC--ACUCACU
.(((((.....((((((.....))))))..................................(((.((((((-.(....).)))))).)))...)--))))... ( -23.40)
>DroPse_CAF1 13343 90 - 1
GAUGUAGAAAAUGCUGCAUAGAACAGCAAAUAUCUAAGAGAAAUUGAAUAUAAAUACGAAAUCAAAUCGA------GUUUGAUCGAGUUUUUAGA--A------
...........(((((.......)))))....((((((((...((((...(((((.(((.......))).------))))).)))).))))))))--.------ ( -16.70)
>DroEre_CAF1 8052 98 - 1
GGAGUGGAAAAUGCUGCAUAGAGCAGCAAAUAUCUAGAAUAAAUUGAAUAUAAAUACGAAAUCAAAUC------GAAUUCUAUUCGACUUGCAGUCUACUCACU
.(((((((...((((((.....))))))...........(((.(((((((..(((.(((.......))------).))).))))))).)))...)))))))... ( -24.40)
>DroYak_CAF1 8185 96 - 1
GGAGUGGAAAAUGCUGCAUAGAGCAGCAAAUAUCUAGAAUAAAUUGAAUAUAAAUACGAAAUCAAAUC------GAAUUCUAUUCGACUUGCAGC--ACUCACU
.(((((.....((((((.....))))))...........(((.(((((((..(((.(((.......))------).))).))))))).)))...)--))))... ( -22.00)
>DroAna_CAF1 13686 95 - 1
GGAGUGGAAAACGCUGCGUGGAGCAGCAAAUAUCUAGAAUAAAUUGAAUAUAAAUACGAAAUCAAAUCGAAUUCGAAUUCGA-------UGCUCC--ACUCGGG
.(((((((....(((((.....)))))......................................(((((((....))))))-------)..)))--))))... ( -27.10)
>DroPer_CAF1 12770 90 - 1
GAUGUAGAAAAUGCUGCAUAGAACAGCAAAUAUCUAAGAGAAAUUGAAUAUAAAUACGAAAUCAAAUCGA------GUUUGAUCGAGUUUUUAGA--A------
...........(((((.......)))))....((((((((...((((...(((((.(((.......))).------))))).)))).))))))))--.------ ( -16.70)
>consensus
GGAGUGGAAAAUGCUGCAUAGAGCAGCAAAUAUCUAGAAUAAAUUGAAUAUAAAUACGAAAUCAAAUCGA____GAAUUCGAUUCGACUUGCAGC__ACUCACU
....((((...((((((.....))))))....)))).................................................................... ( -8.82 =  -9.10 +   0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,385,273 – 3,385,369
Length 96
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 81.58
Mean single sequence MFE -16.29
Consensus MFE -9.85
Energy contribution -9.49
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -1.82
Structure conservation index 0.60
SVM decision value 0.05
SVM RNA-class probability 0.558796
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3385273 96 + 22407834
UGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCCGAUAU--GCUUUCCUUUGGCUGGCGCUUGCCUUG
.((...((((((........(((((...)))))...((((((.....))))))...........)))))--)...))....(((........)))... ( -15.70)
>DroPse_CAF1 13369 93 + 1
UGAUUUCGUAUUUAUAUUCAAUUUCUCUUAGAUAUUUGCUGUUCUAUGCAGCAUUUUCUACAUCGAAAUCUACUUCCACUU----CG-AUUUGCUUUG
.(((((((....................((((....((((((.....))))))...))))...)))))))...........----..-.......... ( -15.40)
>DroSec_CAF1 8082 94 + 1
UGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCCGAUAU--GCUUUCCU-UGGCUCG-GCUUGGCUUG
.......(((((((..............))))))).((((((.....))))))....(((..((((...--(((.....-.))))))-)..))).... ( -19.74)
>DroEre_CAF1 8086 95 + 1
UGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCCGAUAU--GCUUUCCUUUGGCUCA-GCUUGCCUUG
.((...((((((........(((((...)))))...((((((.....))))))...........)))))--)...))....(((...-....)))... ( -15.40)
>DroAna_CAF1 13717 91 + 1
UGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCCACGCAGCGUUUUCCACUCCGUGUU--GCUCCACUACAGCUC-----UGAGUUG
..............................((....((((((.....))))))...)).((((.(.(((--(........)))).)-----.)))).. ( -16.10)
>DroPer_CAF1 12796 93 + 1
UGAUUUCGUAUUUAUAUUCAAUUUCUCUUAGAUAUUUGCUGUUCUAUGCAGCAUUUUCUACAUCGAAAUCUACUUCCACUU----CG-AUUUGCUUUG
.(((((((....................((((....((((((.....))))))...))))...)))))))...........----..-.......... ( -15.40)
>consensus
UGAUUUCGUAUUUAUAUUCAAUUUAUUCUAGAUAUUUGCUGCUCUAUGCAGCAUUUUCCACUCCGAUAU__GCUUCCCUUUGGCUCG_GCUUGCCUUG
.......(((((((..............))))))).((((((.....))))))............................................. ( -9.85 =  -9.49 +  -0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:18 2006