Locus 4268

Sequence ID 3R_DroMel_CAF1
Location 11,398,774 – 11,399,012
Length 238
Max. P 0.987753
window6926 window6927

overview

Window 6

Location 11,398,774 – 11,398,893
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.65
Mean single sequence MFE -32.60
Consensus MFE -20.30
Energy contribution -21.58
Covariance contribution 1.28
Combinations/Pair 1.26
Mean z-score -2.79
Structure conservation index 0.62
SVM decision value 2.09
SVM RNA-class probability 0.987753
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11398774 119 + 27905053
ACAAAACGCAUCAAAGAGGAUGAUCCCAUCCCAUCAAUAAAUCCUGAUGGCAACA-CCCCCACAUGAAAAUCUCUUCAUUGAUGGCGCGGUGUUGGGAAAUCACUUCACUGCACUAAAAU
.......(((.....((((.(((((((...((((((........)))))).((((-((((((((((((......)))).)).))).).))))))))))..)))))))..)))........ ( -33.90)
>DroSec_CAF1 146464 119 + 1
ACAAAACGCAUCAAAGAGGAUUAUCCCAUCCCAUCAAUAAAUCCUGAUGGCAACU-CCCCCAUAUGGAAAUCUCUUCAUUGAUGGCGCGGUGUUGGGAAAUCACUUCACUGCACUAAAAU
.......(((...(((..((((.((((...((((((........)))))).(((.-((((((((((((......)))))..)))).).)).))))))))))).)))...)))........ ( -30.20)
>DroSim_CAF1 137551 119 + 1
ACAAAACGCAUCAAAGAGGAUUAUCCCAUUCCAUCAAUAAAUCCUGAUGGCAACU-CCCCCACGUGGAAAUCUCUUUAUUGAUGGCGCGGUGUUGGGAAAUCACUUCACUGCACUAAAAU
.......(((((((((((((((.(((....((((((........))))))..((.-.......))))))))).)))).))))).))((((((..((.......)).))))))........ ( -28.90)
>DroEre_CAF1 134571 111 + 1
---------AUCGGGGAGGAUUUUCCCCUCCCAACUAGAAAUCCUGCAGGCGGGAGGUGCCACAUUGAAAUCUCCUCAUUGAUGGCGCGCUGUUGGGAAAUCACUUCAGUGCACUAAAAU
---------...((((((....))))))(((((((.((...(((((....))))).((((((((.(((.......))).)).)))))).)))))))))...(((....)))......... ( -40.80)
>DroYak_CAF1 137479 106 + 1
ACAGAACGCAUCACAGAGGAUUAUCCCAUCCCACCGGGAACUCCC--------------CCAUAUCGAAAUGUCUUCAUUGAUGGCGCGGUGUUGGGAAAUCACUUCGCUGCACUAAAAU
.......(((...(..((((((.(((((...(((((((....)))--------------((((.....((((....)))).))))...)))).))))))))).))..).)))........ ( -29.20)
>consensus
ACAAAACGCAUCAAAGAGGAUUAUCCCAUCCCAUCAAUAAAUCCUGAUGGCAACA_CCCCCACAUGGAAAUCUCUUCAUUGAUGGCGCGGUGUUGGGAAAUCACUUCACUGCACUAAAAU
........((((((.(((((..........((((((........)))))).........((....)).....))))).))))))..((((((..((.......)).))))))........ (-20.30 = -21.58 +   1.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,398,893 – 11,399,012
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.69
Mean single sequence MFE -32.34
Consensus MFE -25.54
Energy contribution -26.06
Covariance contribution 0.52
Combinations/Pair 1.07
Mean z-score -1.62
Structure conservation index 0.79
SVM decision value 0.42
SVM RNA-class probability 0.727369
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11398893 119 + 27905053
CCUAUUAAAACCGUGGAUCGUCAGGGCAACAACAA-AGGCGGUGCCAAAAGCAUUAGUCAAGCAUUUUUUUUUCAGCCAUUUUUGGCUCACGGAAAAUGCAAAUUAGUCAGCCCAAACGU
.((((.......))))..(((..((((........-.((((((((.....))))).)))..(((((((((....(((((....)))))...)))))))))..........))))..))). ( -32.70)
>DroSec_CAF1 146583 117 + 1
CCUAUUAAAUCCGUGGAUCGGCAGGGCAACAACAAAAGGCGGUGCCAAAAGCAUUAGUCAAGCAUUUU---UUUAGCCAUUUUUGGCUCACGGAAAAUGCAAAUUAGUCAGCCCAAGCGU
..........(((.....)))..((((..........((((((((.....))))).)))..(((((((---((.(((((....)))))...)))))))))..........))))...... ( -32.90)
>DroSim_CAF1 137670 118 + 1
CCUAUUAAAUCCGUGGAUCGGCAGGGCAACAACAAAAGGCGGUGCCAAAAGCAUUAGUCAAGCAUUUUU--UUUAGCCAUUUUUGGCUCACGGAAAAUGCAAAUUAGUCAGCCCAAACGU
..........(((.....)))..((((..........((((((((.....))))).)))..((((((((--(..(((((....)))))...)))))))))..........))))...... ( -33.30)
>DroEre_CAF1 134682 115 + 1
CGCAUUAAGUCCCUGGAUCUGGUGGGCAGCCGCAA-AGGCGGUGCCAAAAGCAUUAGUCAAGUAUUU----UUUAGCCAUUUUCGGCUCACGGAAAAUGCAAAUUAGUCAGCCCAAACGU
..(((((..((....))..)))))((((.((((..-..))))))))....((((((((...((((((----(((((((......))))...)))))))))..))))))..))........ ( -33.00)
>DroYak_CAF1 137585 115 + 1
CCUAUUAAGUCCGCGGAUCUGCAGGGCAGCAACAA-AGGCGGUGGCAAGAGCAUUAGUCAAGUAUUU----UUUAGCCAUUUUUGGCUCACGGAAAAUGCAAAUUAGUCAGCCCAAACGU
............(((....))).((((........-.(((....((....))....)))..((((((----((((((((....)))))...)))))))))..........))))...... ( -29.80)
>consensus
CCUAUUAAAUCCGUGGAUCGGCAGGGCAACAACAA_AGGCGGUGCCAAAAGCAUUAGUCAAGCAUUUU___UUUAGCCAUUUUUGGCUCACGGAAAAUGCAAAUUAGUCAGCCCAAACGU
........(((....))).....((((..........((((((((.....))))).)))..(((((((......(((((....))))).....)))))))..........))))...... (-25.54 = -26.06 +   0.52)

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 11:24:00 2006