Locus 1127

Sequence ID 2R_DroMel_CAF1
Location 4,516,207 – 4,516,358
Length 151
Max. P 0.869051
window1987 window1988 window1989 window1990

overview

Window 7

Location 4,516,207 – 4,516,298
Length 91
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 92.39
Mean single sequence MFE -31.90
Consensus MFE -29.67
Energy contribution -29.57
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.48
Structure conservation index 0.93
SVM decision value -0.02
SVM RNA-class probability 0.525707
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4516207 91 + 20766785
AAAAGCAGAAGCAGUCGGCAGUGGCAGCGCAAUUGAAACACUUGUACUAAGCUGCUGUUGCUCCUGC-UGUUGGUGGUGGUGGUGGUGCUGG
...(((((.(((((.(((((((...((..(((.((...)).)))..))..)))))))))))).))))-).(..(((.(......).)))..) ( -29.80)
>DroSec_CAF1 50592 86 + 1
AAAAGCAGAAGCAGUCGGCAGUGGCAGCGCAAUUGAAACACUUGUACUAAGCUGCUGCUGCUCCUGCCUGCUGGUGGUGGUG------GUGG
...(((((..((((..(((((..(((((((((.((...)).)))).....)))))..))))).)))))))))..........------.... ( -33.10)
>DroSim_CAF1 49509 92 + 1
AAAAGCAGAAGCAGUCGGCAGUGGCAGCGCAAUUGAAACACUUGUACUAAGCUGCUGUUGCUCCUGCCUGCUGGUGGUGGUGGUGCUGGUGG
....((((.(((((.(((((((...((..(((.((...)).)))..))..)))))))))))).))))(..(..((.........))..)..) ( -32.80)
>consensus
AAAAGCAGAAGCAGUCGGCAGUGGCAGCGCAAUUGAAACACUUGUACUAAGCUGCUGUUGCUCCUGCCUGCUGGUGGUGGUGGUG_UGGUGG
...(((((..((((..(((((..(((((((((.((...)).)))).....)))))..))))).))))))))).................... (-29.67 = -29.57 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,516,207 – 4,516,298
Length 91
Sequences 3
Columns 92
Reading direction reverse
Mean pairwise identity 92.39
Mean single sequence MFE -25.87
Consensus MFE -23.27
Energy contribution -23.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.90
SVM decision value 0.86
SVM RNA-class probability 0.869051
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4516207 91 - 20766785
CCAGCACCACCACCACCACCAACA-GCAGGAGCAACAGCAGCUUAGUACAAGUGUUUCAAUUGCGCUGCCACUGCCGACUGCUUCUGCUUUU
.......................(-(((((((((.(.((((..(((..(((.........)))..)))...)))).)..))))))))))... ( -23.90)
>DroSec_CAF1 50592 86 - 1
CCAC------CACCACCACCAGCAGGCAGGAGCAGCAGCAGCUUAGUACAAGUGUUUCAAUUGCGCUGCCACUGCCGACUGCUUCUGCUUUU
....------.............(((((((((((((.((((..(((..(((.........)))..)))...)))).).)))))))))))).. ( -29.20)
>DroSim_CAF1 49509 92 - 1
CCACCAGCACCACCACCACCAGCAGGCAGGAGCAACAGCAGCUUAGUACAAGUGUUUCAAUUGCGCUGCCACUGCCGACUGCUUCUGCUUUU
......((.............))(((((((((((.(.((((..(((..(((.........)))..)))...)))).)..))))))))))).. ( -24.52)
>consensus
CCACCA_CACCACCACCACCAGCAGGCAGGAGCAACAGCAGCUUAGUACAAGUGUUUCAAUUGCGCUGCCACUGCCGACUGCUUCUGCUUUU
.......................(((((((((((...((((..(((..(((.........)))..)))...))))....))))))))))).. (-23.27 = -23.60 +   0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,516,268 – 4,516,358
Length 90
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 92.31
Mean single sequence MFE -32.03
Consensus MFE -25.99
Energy contribution -25.77
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.00
Structure conservation index 0.81
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4516268 90 + 20766785
UCCUGC-UGUUGGUGGUGGUGGUGGUGCUGGUGCCCCAACUCUUGUGGCACGCCGCUUUGGCUCGCUUGCAUUUUACAGGAAUUUCAAUAA
(((((.-(((.((((((.(.((((((....(((((.((.....)).))))))))))).).)).)))).))).....))))).......... ( -30.10)
>DroSec_CAF1 50653 85 + 1
UCCUGCCUGCUGGUGGUGGUG------GUGGUGCCACAACUCUUGUGGCACGCCGCUUUGGCUCGCUUGCAUUUUACAGGAAUUUCAAUAA
(((((..(((.((((((((((------(((.(((((((.....))))))))))))))...)).)))).))).....))))).......... ( -35.50)
>DroSim_CAF1 49570 91 + 1
UCCUGCCUGCUGGUGGUGGUGGUGCUGGUGGUGCCCCAACUCUUGUGGCACGCCGCUUUGGCUCGCUUGCAUUUUACAGGAAUUUCAAUAA
(((((((....))).((((.(((((.(((((((((.((.....)).)))))(((.....))).)))).))))))))))))).......... ( -30.50)
>consensus
UCCUGCCUGCUGGUGGUGGUGGUG_UGGUGGUGCCCCAACUCUUGUGGCACGCCGCUUUGGCUCGCUUGCAUUUUACAGGAAUUUCAAUAA
(((((..(((.(((((..............(((((.((.....)).)))))(((.....)))))))).))).....))))).......... (-25.99 = -25.77 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,516,268 – 4,516,358
Length 90
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 92.31
Mean single sequence MFE -26.51
Consensus MFE -22.87
Energy contribution -23.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.86
SVM decision value 0.35
SVM RNA-class probability 0.699483
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4516268 90 - 20766785
UUAUUGAAAUUCCUGUAAAAUGCAAGCGAGCCAAAGCGGCGUGCCACAAGAGUUGGGGCACCAGCACCACCACCACCACCAACA-GCAGGA
..........((((((.........(((.(((.....))).))).......(((((((.................)).))))).-)))))) ( -22.53)
>DroSec_CAF1 50653 85 - 1
UUAUUGAAAUUCCUGUAAAAUGCAAGCGAGCCAAAGCGGCGUGCCACAAGAGUUGUGGCACCAC------CACCACCACCAGCAGGCAGGA
..........((((((....(((......(((.....)))((((((((.....))))))))...------...........))).)))))) ( -30.10)
>DroSim_CAF1 49570 91 - 1
UUAUUGAAAUUCCUGUAAAAUGCAAGCGAGCCAAAGCGGCGUGCCACAAGAGUUGGGGCACCACCAGCACCACCACCACCAGCAGGCAGGA
..........((((((....(((..(((.(((.....))).))).......((((((....).))))).............))).)))))) ( -26.90)
>consensus
UUAUUGAAAUUCCUGUAAAAUGCAAGCGAGCCAAAGCGGCGUGCCACAAGAGUUGGGGCACCACCA_CACCACCACCACCAGCAGGCAGGA
..........((((((....(((......(((.....)))(((((.((.....)).)))))....................))).)))))) (-22.87 = -23.20 +   0.33)

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 09:57:12 2006