Locus 1483

Sequence ID 2R_DroMel_CAF1
Location 5,639,681 – 5,639,840
Length 159
Max. P 0.935462
window2521 window2522

overview

Window 1

Location 5,639,681 – 5,639,800
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.80
Mean single sequence MFE -28.76
Consensus MFE -22.02
Energy contribution -22.26
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.77
SVM decision value 0.33
SVM RNA-class probability 0.692023
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5639681 119 - 20766785
UACACCCCGCCAUAUAGUAUAAUUAGCAAUUGAACUAUAUAUUUAUAUGUGCCUCAAGGCAAACGGAUUUCGCUUG-AAAAAUGUAGUCACUCAAUUGUAGGGAGCUUUAAAGGCGGCUG
......(((((....(((....(..(((((((((((((((.........((((....))))......((((....)-))).)))))))...))))))))..)..))).....)))))... ( -29.00)
>DroSec_CAF1 6374 119 - 1
UACACCCCGCCAUAUAGUAUAAUUAGCAAUUGAACUAUAUAUUUAUAUGUGCCUCAAGGCAAACAGAUUUCGCUUG-AAAAAUGUAGUCACUCAAUUGUAGGGAGCUUUAAAGGCGGCUG
......(((((....(((....(..(((((((((((((((.........((((....))))......((((....)-))).)))))))...))))))))..)..))).....)))))... ( -29.00)
>DroSim_CAF1 6444 119 - 1
UACACCCCGCCAUAUAGUAUAAUUAGCAAUUGAACUAUAUAUUUAUAUGUGCCUCAAGGCAAACAGAUUUCGCUCG-AAAAAUGUAGUCACUCAAUUGUAGGGAGCUUUAAAGGCGGCUG
......(((((....(((....(..(((((((((((((((.........((((....))))......((((....)-))).)))))))...))))))))..)..))).....)))))... ( -29.90)
>DroEre_CAF1 6799 118 - 1
UACACCCCGCCAUAUAGUAUAAUUAGCAAUUGAACUAUAUAUUUAUAUUUGCCUCAAGGCAAACAGAUUUUGCUUG-AAAAAUGUAAUCACCCA-CUGAAAGGAGCUUUAAAGGCGGCUG
......((((((((((((.((((.....)))).)))))))..((((((((...(((((.((((.....))))))))-).)))))))).......-((....)).........)))))... ( -26.90)
>DroYak_CAF1 6396 120 - 1
UACACCCCGCCAUAUAGUAUAAUUAGCAAUUGAACUAUAUAUUUAUAUUUGCCUCAAGGCAAACAGAUUUUGCUUGGAAAAAUGUAAUCACCCAAUUGUAAGGAGCUUGGGAGGCGACAG
.......(((((((((((.((((.....)))).)))))))..((((((((...((.(((((((.....))))))).)).))))))))...(((((..((.....))))))).)))).... ( -29.00)
>consensus
UACACCCCGCCAUAUAGUAUAAUUAGCAAUUGAACUAUAUAUUUAUAUGUGCCUCAAGGCAAACAGAUUUCGCUUG_AAAAAUGUAGUCACUCAAUUGUAGGGAGCUUUAAAGGCGGCUG
......((((((((((((.((((.....)))).))))))).........((((....))))..........((((....((.((........)).)).....))))......)))))... (-22.02 = -22.26 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,639,721 – 5,639,840
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.15
Mean single sequence MFE -28.42
Consensus MFE -23.98
Energy contribution -24.58
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.84
SVM decision value 1.24
SVM RNA-class probability 0.935462
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5639721 119 + 20766785
UUU-CAAGCGAAAUCCGUUUGCCUUGAGGCACAUAUAAAUAUAUAGUUCAAUUGCUAAUUAUACUAUAUGGCGGGGUGUAUCAUAUAACGAAUUUGUGGUAGACAGAUAGUGGGAAAAAC
(((-(..((....(((((.((((....))))((((((..((((((((......))))..)))).)))))))))))((.(((((((.........))))))).)).....))..))))... ( -28.90)
>DroSec_CAF1 6414 119 + 1
UUU-CAAGCGAAAUCUGUUUGCCUUGAGGCACAUAUAAAUAUAUAGUUCAAUUGCUAAUUAUACUAUAUGGCGGGGUGUAUCAUAUAACGAAUUUGUGGUAGACAGAUAGAGGGAAAAAC
(((-(...(...(((((((((((.(((.((((.......((((((((..(((.....)))..)))))))).....)))).)))....(((....)))))))))))))).)...))))... ( -29.00)
>DroSim_CAF1 6484 119 + 1
UUU-CGAGCGAAAUCUGUUUGCCUUGAGGCACAUAUAAAUAUAUAGUUCAAUUGCUAAUUAUACUAUAUGGCGGGGUGUAUCAUAUAACGAAUUUGUGGUAGACAGAUAGAGGGAAAAAC
(((-(...(...(((((((((((.(((.((((.......((((((((..(((.....)))..)))))))).....)))).)))....(((....)))))))))))))).)...))))... ( -27.90)
>DroEre_CAF1 6838 119 + 1
UUU-CAAGCAAAAUCUGUUUGCCUUGAGGCAAAUAUAAAUAUAUAGUUCAAUUGCUAAUUAUACUAUAUGGCGGGGUGUAUCAUAUAACGAAAUUGUGGUAGACAGAUAGAGGGAAAAAC
(((-(..((......((((((((....))))))))....((((((((..(((.....)))..))))))))))...((.(((((((.........))))))).)).........))))... ( -26.50)
>DroYak_CAF1 6436 120 + 1
UUUCCAAGCAAAAUCUGUUUGCCUUGAGGCAAAUAUAAAUAUAUAGUUCAAUUGCUAAUUAUACUAUAUGGCGGGGUGUAUCAUAUAACGAAAUUGUGGUAGACAGAUAGAGGGAAAAAC
(((((..((......((((((((....))))))))....((((((((..(((.....)))..))))))))))...((.(((((((.........))))))).))........)))))... ( -29.80)
>consensus
UUU_CAAGCGAAAUCUGUUUGCCUUGAGGCACAUAUAAAUAUAUAGUUCAAUUGCUAAUUAUACUAUAUGGCGGGGUGUAUCAUAUAACGAAUUUGUGGUAGACAGAUAGAGGGAAAAAC
............(((((((((((.(((.((((.......((((((((..(((.....)))..)))))))).....)))).)))....(((....))))))))))))))............ (-23.98 = -24.58 +   0.60)

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 10:05:56 2006