Locus 7618

Sequence ID X_DroMel_CAF1
Location 19,005,871 – 19,006,006
Length 135
Max. P 0.998063
window12505 window12506 window12507 window12508

overview

Window 5

Location 19,005,871 – 19,005,981
Length 110
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 89.81
Mean single sequence MFE -23.13
Consensus MFE -18.01
Energy contribution -17.64
Covariance contribution -0.37
Combinations/Pair 1.15
Mean z-score -2.28
Structure conservation index 0.78
SVM decision value 1.01
SVM RNA-class probability 0.899939
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19005871 110 + 22224390
UAUAGAAAAUCAUCACUUCCUGGCACAUUGAAAAUCACACAAUUCAAACAGCUCGCGUCAAGCGCCAUUUGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGAC
....................((((...(((((..........))))).......((.....))))))...((((((((((((........((....)))))))))))))) ( -23.00)
>DroSec_CAF1 28327 106 + 1
UAUAGAAUAUCAUCACUUCCUGGCACUUUGGAAAUCGCA---UUCAAACAACUCGCGUCAAGCGCCAU-UGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGGC
....................((((..((((((.......---))))))......((.....)))))).-.((((((((((((........((....)))))))))))))) ( -22.90)
>DroSim_CAF1 22923 106 + 1
UAUAGAAAAUCAUCACUUCCUGGCACUUUGGAAAUCGCA---UUCAAACAGCUCGCGUCAAGCGCCAU-UGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGGC
....................((((..((((((.......---))))))......((.....)))))).-.((((((((((((........((....)))))))))))))) ( -22.90)
>DroYak_CAF1 28535 102 + 1
UACAGAAAAUCACCAUUUCCUGGC----CGCCAAUCGCA---UUCAAACAACUCGCGUCAAGCGCCAU-UGUCAAUGUAUCUAAAUGCUUGAGCAAUCAGAUACUUUGAC
....................((((----.((....(((.---............)))....)))))).-.(((((.((((((.(.(((....))).).)))))).))))) ( -23.72)
>consensus
UAUAGAAAAUCAUCACUUCCUGGCACUUUGGAAAUCGCA___UUCAAACAACUCGCGUCAAGCGCCAU_UGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGAC
....................((((....((.....)).................((.....))))))...((((((((((((................)))))))))))) (-18.01 = -17.64 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,005,871 – 19,005,981
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 89.81
Mean single sequence MFE -35.95
Consensus MFE -30.20
Energy contribution -31.20
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -3.80
Structure conservation index 0.84
SVM decision value 2.23
SVM RNA-class probability 0.990829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19005871 110 - 22224390
GUCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACAAAUGGCGCUUGACGCGAGCUGUUUGAAUUGUGUGAUUUUCAAUGUGCCAGGAAGUGAUGAUUUUCUAUA
((((((((((((((.(((....))).))))))))))))))....((((((((((((((..........)))))......)))).)))))(((((((....)))))))... ( -37.80)
>DroSec_CAF1 28327 106 - 1
GCCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACA-AUGGCGCUUGACGCGAGUUGUUUGAA---UGCGAUUUCCAAAGUGCCAGGAAGUGAUGAUAUUCUAUA
..((((((((((((.(((....))).))))))))))))...-.((((((((...(.(((((((.....---.))))))).).))))))))((((.........))))... ( -34.60)
>DroSim_CAF1 22923 106 - 1
GCCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACA-AUGGCGCUUGACGCGAGCUGUUUGAA---UGCGAUUUCCAAAGUGCCAGGAAGUGAUGAUUUUCUAUA
..((((((((((((.(((....))).))))))))))))...-..(((((((..((((..(.....)..---)))).......)))))))(((((((....)))))))... ( -34.30)
>DroYak_CAF1 28535 102 - 1
GUCAAAGUAUCUGAUUGCUCAAGCAUUUAGAUACAUUGACA-AUGGCGCUUGACGCGAGUUGUUUGAA---UGCGAUUGGCG----GCCAGGAAAUGGUGAUUUUCUGUA
(((((.((((((((.(((....))).)))))))).))))).-...........(((.((((((.....---.)))))).)))----..((((((((....)))))))).. ( -37.10)
>consensus
GCCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACA_AUGGCGCUUGACGCGAGCUGUUUGAA___UGCGAUUUCCAAAGUGCCAGGAAGUGAUGAUUUUCUAUA
((((((((((((((.(((....))).))))))))))))))....((((((((.((((...(......)...)))).....))).)))))(((((((....)))))))... (-30.20 = -31.20 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,005,911 – 19,006,006
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 88.41
Mean single sequence MFE -23.04
Consensus MFE -18.59
Energy contribution -18.67
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -2.47
Structure conservation index 0.81
SVM decision value 2.09
SVM RNA-class probability 0.987589
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19005911 95 + 22224390
AAUUCAAACAGCUCGCGUCAAGCGCCAUUUGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGACACCUGCGCCUGCAAUCCGAAUCGUU
............(((.((((.((((....(((((((((((((........((....)))))))))))))))...)))).))..)).)))...... ( -25.00)
>DroSec_CAF1 28366 92 + 1
--UUCAAACAACUCGCGUCAAGCGCCAU-UGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGGCACCUCCGCCUGCAAUCCGAAUCGUU
--..........(((.((((.(((....-(((((((((((((........((....)))))))))))))))....))).))..)).)))...... ( -21.40)
>DroSim_CAF1 22962 92 + 1
--UUCAAACAGCUCGCGUCAAGCGCCAU-UGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGGCACCUCCGCCUGCAAUCCGAAUCGUU
--..........(((.((((.(((....-(((((((((((((........((....)))))))))))))))....))).))..)).)))...... ( -21.40)
>DroEre_CAF1 27380 82 + 1
------------UCGGCGCAAGCGGCAU-UGCCAAAGUAUCUAAAUACUUGAGCCAUCAGAUACUUUGACACCUCCGUCUGCAAUCCGAAUCGUG
------------((((.(((..(((...-((.((((((((((................)))))))))).))...)))..)))...))))...... ( -25.49)
>DroYak_CAF1 28570 92 + 1
--UUCAAACAACUCGCGUCAAGCGCCAU-UGUCAAUGUAUCUAAAUGCUUGAGCAAUCAGAUACUUUGACACCUCCGCCUGCAAUCCGAAUCGUG
--..........(((.((((.(((....-((((((.((((((.(.(((....))).).)))))).))))))....))).))..)).)))...... ( -21.90)
>consensus
__UUCAAACAACUCGCGUCAAGCGCCAU_UGUCAAAGUAUCUAAAUACUUGAGCAAUCAGAUACUUUGACACCUCCGCCUGCAAUCCGAAUCGUU
............(((...((.(((.....(((((((((((((................)))))))))))))....))).)).....)))...... (-18.59 = -18.67 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,005,911 – 19,006,006
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 88.41
Mean single sequence MFE -37.76
Consensus MFE -29.02
Energy contribution -30.58
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -5.03
Structure conservation index 0.77
SVM decision value 3.00
SVM RNA-class probability 0.998063
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19005911 95 - 22224390
AACGAUUCGGAUUGCAGGCGCAGGUGUCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACAAAUGGCGCUUGACGCGAGCUGUUUGAAUU
...(((((((((..(((((((...(((((((((((((((.(((....))).)))))))))))))))....))))))).(....)..))))))))) ( -41.90)
>DroSec_CAF1 28366 92 - 1
AACGAUUCGGAUUGCAGGCGGAGGUGCCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACA-AUGGCGCUUGACGCGAGUUGUUUGAA--
(((((((((.....((((((....((.((((((((((((.(((....))).)))))))))))).))-....))))))...)))))))))....-- ( -36.20)
>DroSim_CAF1 22962 92 - 1
AACGAUUCGGAUUGCAGGCGGAGGUGCCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACA-AUGGCGCUUGACGCGAGCUGUUUGAA--
.....(((((((.((..(((.((((((((((((((((((.(((....))).)))))))))).....-.))))))))..)))..)).)))))))-- ( -36.00)
>DroEre_CAF1 27380 82 - 1
CACGAUUCGGAUUGCAGACGGAGGUGUCAAAGUAUCUGAUGGCUCAAGUAUUUAGAUACUUUGGCA-AUGCCGCUUGCGCCGA------------
......((((...(((..(((...(((((((((((((((..((....))..)))))))))))))))-...)))..))).))))------------ ( -36.20)
>DroYak_CAF1 28570 92 - 1
CACGAUUCGGAUUGCAGGCGGAGGUGUCAAAGUAUCUGAUUGCUCAAGCAUUUAGAUACAUUGACA-AUGGCGCUUGACGCGAGUUGUUUGAA--
.((((((((.....((((((....((((((.((((((((.(((....))).)))))))).))))))-....))))))...)))))))).....-- ( -38.50)
>consensus
AACGAUUCGGAUUGCAGGCGGAGGUGUCAAAGUAUCUGAUUGCUCAAGUAUUUAGAUACUUUGACA_AUGGCGCUUGACGCGAGCUGUUUGAA__
.(((.((((.....((((((....(((((((((((((((.(((....))).))))))))))))))).....))))))...)))).)))....... (-29.02 = -30.58 +   1.56)

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 12:43:34 2006