Locus 5988

Sequence ID 2L_DroMel_CAF1
Location 16,871,233 – 16,871,366
Length 133
Max. P 0.757444
window9515 window9516

overview

Window 5

Location 16,871,233 – 16,871,329
Length 96
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 65.75
Mean single sequence MFE -27.29
Consensus MFE -11.02
Energy contribution -13.91
Covariance contribution 2.89
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.40
SVM decision value 0.49
SVM RNA-class probability 0.757444
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16871233 96 - 22407834
AACUGUCGCCUGCCCUUAUGUACCCAAAAAGAAAAAGAAA--AACCAUGUAUAUAUGGGUUGGAUGAGGGAGGAAGGGAGGGUGGCGGUCCACCAGCC
.((((((((((.(((((.....(((...............--..(((((....))))).((....)))))...))))).))))))))))......... ( -29.30)
>DroSec_CAF1 10559 88 - 1
AACUGUCGCCUGCCCUUAUGUACUCAAAAA--------AA--AACCAUAUAUAAACCGUAUAUAAGGGGGGGGGGGGGGGGGUGGUGCUCCACCAACC
..((.((.(((.(((((((((((.......--------..--...............))))))))))).))).)).))..(((((....))))).... ( -34.26)
>DroEre_CAF1 42842 80 - 1
AACUGUCGCCUGCCCUUAUGUACCCAAAAAAAAAAAAAAAAUAAACGU---------GUAUAUAUGGGGUGGUU---------GGGGGUCCACCAACU
.(((.(((.(..(((((((((((.(.....................).---------))))))).))))..).)---------)).)))......... ( -18.30)
>consensus
AACUGUCGCCUGCCCUUAUGUACCCAAAAA_AAAAA_AAA__AACCAU_UAUA_A__GUAUAUAUGGGGGGGGA_GGG_GGGUGGCGGUCCACCAACC
........(((.(((((((((((..................................))))))).)))).)))...((..(((((....)))))..)) (-11.02 = -13.91 +   2.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,871,256 – 16,871,366
Length 110
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -23.66
Consensus MFE -13.42
Energy contribution -14.86
Covariance contribution 1.44
Combinations/Pair 1.05
Mean z-score -1.87
Structure conservation index 0.57
SVM decision value 0.13
SVM RNA-class probability 0.598164
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16871256 110 - 22407834
CAAGACCGAAAGAGAAAAGCCCGAGAAAAUUGCGCAGAACUGUCGCCUGCCCUUAUGUACCCAAAAAGAAAAAGAAA--AACCAUGUAUAUAUGGGUUGGAUGAGGGAGGAA
...((((....)......((.(((.....))).))......))).(((.(((((((.((((((..............--.............)))).)).)))))))))).. ( -25.33)
>DroSec_CAF1 10582 102 - 1
CAAGACCGAAAGAGAAAAGCCCGAGAAAAUUGCGCAGAACUGUCGCCUGCCCUUAUGUACUCAAAAA--------AA--AACCAUAUAUAAACCGUAUAUAAGGGGGGGGGG
......(....).......(((.........(((((....)).)))((.(((((((((((.......--------..--...............))))))))))).))))). ( -26.66)
>DroSim_CAF1 13113 93 - 1
CAAGACCGAAAGAGAAAAGCCCGAGAAAAUUGCGCAGAACUGUCGCCUGCCCUUAUGUACUCAAAAA-------AAA--AACCAU---------GUAUAUAAGGGGGGGAG-
...((((....)......((.(((.....))).))......))).(((.(((((((((((.......-------...--......---------))))))))))).)))..- ( -27.29)
>DroEre_CAF1 42857 102 - 1
CAAGACCGAAGGAGAAAAGCCCGAGAAAAUUGCGCAGAACUGUCGCCUGCCCUUAUGUACCCAAAAAAAAAAAAAAAAUAAACGU---------GUAUAUAUGGGGUGGUU-
...((((..(((.((...((.(((.....))).)).......)).)))((((((((((((.(.....................).---------))))))).)))))))))- ( -19.50)
>DroYak_CAF1 5978 94 - 1
CAAGACCGAAAGAGAAAAGCCCGAGAAAAUUGCGCAGAACUGUCGCCUGCCCUUAUGUACCCAAAA--------AAAAUAAACGU---------GUAUAUACUGGGUGGUU-
...((((....)......((.(((.....))).))......)))(((.((((.(((((((.(....--------.........).---------)))))))..))))))).- ( -19.52)
>consensus
CAAGACCGAAAGAGAAAAGCCCGAGAAAAUUGCGCAGAACUGUCGCCUGCCCUUAUGUACCCAAAAA_______AAA__AACCAU_________GUAUAUAAGGGGGGGGG_
...((((....)......((.(((.....))).))......))).(((.(((.(((((((..................................))))))).))).)))... (-13.42 = -14.86 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:17 2006