Locus 9797

Sequence ID 3R_DroMel_CAF1
Location 26,029,727 – 26,029,829
Length 102
Max. P 0.959021
window15642 window15643

overview

Window 2

Location 26,029,727 – 26,029,829
Length 102
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 82.86
Mean single sequence MFE -28.70
Consensus MFE -20.50
Energy contribution -21.38
Covariance contribution 0.88
Combinations/Pair 1.16
Mean z-score -2.38
Structure conservation index 0.71
SVM decision value 1.50
SVM RNA-class probability 0.959021
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26029727 102 + 27905053
CUAGAAAAUAUUUUUCGAAGACGAUUU-U-AAAACCGGAAAGCAGUAUUUCGGUUAUCGCAGCAGUUUAGUAUUUGCGCCUUGAACGCUAGACACUGCGAUAUU------
...((((.....))))...........-.-..((((((((.......))))))))(((((((..((((((..(((.......)))..)))))).)))))))...------ ( -25.80)
>DroSec_CAF1 23281 102 + 1
GUAGAAAACUUUUUUCGAAGCCGUUUU-U-AAAACCGGAAAGCAGUAUUUCGGUUAUCGCAGCAGUUGAGUAUUUGUGCCUCAAACUCUAGACGCUGCGGUAUU------
.((((((.((((....))))...))))-)-).((((((((.......))))))))((((((((.(((.((..((((.....))))..)).)))))))))))...------ ( -27.50)
>DroSim_CAF1 24526 102 + 1
GUAGAAAACUUUUUUCGAAGCCGAUUU-U-AAAACCGGAAAGCAGUAUUUCGGUUAUCGCAGCAGUUGAGUGUUUGUGCCUUAAACGCUAGACGCUGCGAUAUU------
..............(((....)))...-.-..((((((((.......))))))))((((((((.(((.((((((((.....)))))))).)))))))))))...------ ( -32.60)
>DroYak_CAF1 23398 108 + 1
GUAGAAGACUUUUUUCGAAGCCGAUUUUUAAAAACCGGAAAGCCACACUUCGCUUAUCGCAGCAGUUGAACAUUUCUGUCUAAAA--CUAAACGCUGCGAUAAGCCUAAA
...((((.((((....))))(((.(((....))).))).........))))((((((((((((((((..(((....)))....))--))....))))))))))))..... ( -28.90)
>consensus
GUAGAAAACUUUUUUCGAAGCCGAUUU_U_AAAACCGGAAAGCAGUAUUUCGGUUAUCGCAGCAGUUGAGUAUUUGUGCCUUAAACGCUAGACGCUGCGAUAUU______
...(((((...)))))................((((((((.......))))))))((((((((.(((.(((.((((.....)))).))).)))))))))))......... (-20.50 = -21.38 +   0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 26,029,727 – 26,029,829
Length 102
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 82.86
Mean single sequence MFE -25.88
Consensus MFE -18.88
Energy contribution -19.62
Covariance contribution 0.75
Combinations/Pair 1.16
Mean z-score -1.98
Structure conservation index 0.73
SVM decision value 0.84
SVM RNA-class probability 0.864072
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26029727 102 - 27905053
------AAUAUCGCAGUGUCUAGCGUUCAAGGCGCAAAUACUAAACUGCUGCGAUAACCGAAAUACUGCUUUCCGGUUUU-A-AAAUCGUCUUCGAAAAAUAUUUUCUAG
------..(((((((((((.((((((.....))))......)).)).)))))))))(((((((......))).))))...-.-...(((....))).............. ( -20.10)
>DroSec_CAF1 23281 102 - 1
------AAUACCGCAGCGUCUAGAGUUUGAGGCACAAAUACUCAACUGCUGCGAUAACCGAAAUACUGCUUUCCGGUUUU-A-AAAACGGCUUCGAAAAAAGUUUUCUAC
------.....((((((((..((.(((((.....))))).))..)).))))))......((((.(((..((((.((((..-.-.....))))..))))..)))))))... ( -22.00)
>DroSim_CAF1 24526 102 - 1
------AAUAUCGCAGCGUCUAGCGUUUAAGGCACAAACACUCAACUGCUGCGAUAACCGAAAUACUGCUUUCCGGUUUU-A-AAAUCGGCUUCGAAAAAAGUUUUCUAC
------..(((((((((((..((.((((.......)))).))..)).)))))))))...((((.(((..(((((((((..-.-.)))))).....)))..)))))))... ( -25.50)
>DroYak_CAF1 23398 108 - 1
UUUAGGCUUAUCGCAGCGUUUAG--UUUUAGACAGAAAUGUUCAACUGCUGCGAUAAGCGAAGUGUGGCUUUCCGGUUUUUAAAAAUCGGCUUCGAAAAAAGUCUUCUAC
.....((((((((((((....((--((...((((....)))).))))))))))))))))..((...(((((((((((((....)))))))........))))))..)).. ( -35.90)
>consensus
______AAUAUCGCAGCGUCUAGCGUUUAAGGCACAAAUACUCAACUGCUGCGAUAACCGAAAUACUGCUUUCCGGUUUU_A_AAAUCGGCUUCGAAAAAAGUUUUCUAC
........(((((((((((..((.(((((.....))))).))..)).)))))))))...((((......((((((((((....)))))))....)))......))))... (-18.88 = -19.62 +   0.75)

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 13:42:21 2006