Locus 3439

Sequence ID 3R_DroMel_CAF1
Location 9,329,201 – 9,329,338
Length 137
Max. P 0.852784
window5517 window5518

overview

Window 7

Location 9,329,201 – 9,329,309
Length 108
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 89.41
Mean single sequence MFE -26.86
Consensus MFE -20.05
Energy contribution -20.09
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.65
Structure conservation index 0.75
SVM decision value 0.13
SVM RNA-class probability 0.597311
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9329201 108 + 27905053
GGCGGUGGUAAAAGUUUUCAUAUUUAAUUUGAGGGCCACCCACUCCAUCGACCAUCGAUGGUGC--CACGAACCAACGAACCCCCCCCCCCCCCCCCCAUUGAGUUUUCC
(((((((((..(((((.........)))))....))))))....((((((.....)))))).))--)..(((((((.(...................).))).))))... ( -24.51)
>DroSec_CAF1 99949 98 + 1
GGCGGUGGUAAAAGUUUUCAUAUUUAAUUUGAGGGCCACCCACUCCAUCGACCAUCGAUGGUGCCCCACGAACCAACGAACCC------------CCCAUUGAGUUUUCC
(((((((((..(((((.........)))))....))))))....((((((.....)))))).)))....(((((((.(.....------------..).))).))))... ( -24.90)
>DroSim_CAF1 102243 98 + 1
GGCGGUGGUAAAAGUUUUCAUAUUUAAUUUGAGGGCCACCCACUCCAUCGACCAUCGAUGGUGCCCCACGAACCAACGAACCC------------CCCAUUGAGUUUUCC
(((((((((..(((((.........)))))....))))))....((((((.....)))))).)))....(((((((.(.....------------..).))).))))... ( -24.90)
>DroEre_CAF1 101437 93 + 1
GGCGGCGGUAAAAGUUUUCAUAUUUAAUUUGAGGGCCACCCACACCACCGACCAUCGAUGGAGC--CACGAACCACUG--CCC------------CCCAUUGAGUU-UCC
(((((.(((....(((((((.........)))))))........(((.((.....)).)))...--.....))).)))--)).------------...........-... ( -21.90)
>DroYak_CAF1 101683 94 + 1
GGCGGUGGUAAAAGUUUUCAUAUUUAAUUUGAGGGCCACCCACUCCAUCGACCAUCGAUGGAGC--CAGGAACCACCG--CCC------------CCCAUUGAGUUUUCC
(((((((((....(((((((.........)))))))..((..((((((((.....)))))))).--..)).)))))))--)).------------............... ( -38.10)
>consensus
GGCGGUGGUAAAAGUUUUCAUAUUUAAUUUGAGGGCCACCCACUCCAUCGACCAUCGAUGGUGC__CACGAACCAACGAACCC____________CCCAUUGAGUUUUCC
((((((((.....(((((((.........)))))))........)))))).)).(((((((...................................)))))))....... (-20.05 = -20.09 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,329,240 – 9,329,338
Length 98
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -25.02
Consensus MFE -17.63
Energy contribution -17.67
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.70
SVM decision value 0.80
SVM RNA-class probability 0.852784
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9329240 98 + 27905053
CCACUCCAUCGACCAUCGAUGGUGC--CACGAACCAACGAACCCCCCCCCCCCCCCCCCAUUGAGUUUUCCCGUACACA--GCGGAAAACACACGGCGG-CUC
((...((((((.....)))))).((--(.((......)).........................(((((((.((.....--)))))))))....)))))-... ( -23.60)
>DroSec_CAF1 99988 90 + 1
CCACUCCAUCGACCAUCGAUGGUGCCCCACGAACCAACGAACCC------------CCCAUUGAGUUUUCCCGUAGACAGAGCGGAAAACACACGGCGG-CUC
.....((((((.....)))))).(((((.((......)).....------------........(((((((.((.......)))))))))....)).))-).. ( -24.50)
>DroSim_CAF1 102282 90 + 1
CCACUCCAUCGACCAUCGAUGGUGCCCCACGAACCAACGAACCC------------CCCAUUGAGUUUUCCCGUACACAGAGCGGAAAACACACGGCGG-CUC
.....((((((.....)))))).(((((.((......)).....------------........(((((((.((.......)))))))))....)).))-).. ( -24.50)
>DroEre_CAF1 101476 84 + 1
CCACACCACCGACCAUCGAUGGAGC--CACGAACCACUG--CCC------------CCCAUUGAGUU-UCCCGUACACA--GCGGAAAACACACGGCGGCCUC
.....((.(((....(((((((.((--...........)--)..------------.)))))))(((-(.((((.....--)))).))))...))).)).... ( -22.30)
>DroYak_CAF1 101722 84 + 1
CCACUCCAUCGACCAUCGAUGGAGC--CAGGAACCACCG--CCC------------CCCAUUGAGUUUUCCCGUACACA--GCGGAAAACACACGGCGG-CUC
((.((((((((.....)))))))).--..)).....(((--((.------------.....((.(((((((.((.....--))))))))).)).)))))-... ( -30.20)
>consensus
CCACUCCAUCGACCAUCGAUGGUGC__CACGAACCAACGAACCC____________CCCAUUGAGUUUUCCCGUACACA__GCGGAAAACACACGGCGG_CUC
........(((.((.(((((((...................................)))))))(((((((.((.......)))))))))....))))).... (-17.63 = -17.67 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:01 2006