Locus 8270

Sequence ID 3L_DroMel_CAF1
Location 21,723,652 – 21,723,881
Length 229
Max. P 0.999859
window13522 window13523 window13524 window13525 window13526

overview

Window 2

Location 21,723,652 – 21,723,766
Length 114
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 96.08
Mean single sequence MFE -45.40
Consensus MFE -42.49
Energy contribution -42.60
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.94
SVM decision value 0.47
SVM RNA-class probability 0.748272
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21723652 114 - 23771897
AAUCGAUGGCAGUGCCGCCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUCAGCUUCAGCUGCAGCCUUAGCUUGCGAUUGCGAUU-----
(((((..(((.(((((..(((......))).))))).........(((..((((...))))((((((((((((....)))))..))))))).)))...)))..)))))......----- ( -41.80)
>DroSec_CAF1 5564 119 - 1
AAUCGAUGGCAGUGCCGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUCAGCUUCAGCUGCAGCCUUAGCCUGCGAUUGCGAUUGCCGC
((((((((.(.(((((.((((......)))))))))..(.....)).))))))))....((((((((((((((..((.((((....)))).))..)))))).((....)))))))))). ( -47.20)
>DroSim_CAF1 10583 119 - 1
AAUCGAUGGCAGUGCCGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUCAGCUUCAGCUGCAGCCUUAGCCUGCGAUUGCGAUUGCCGC
((((((((.(.(((((.((((......)))))))))..(.....)).))))))))....((((((((((((((..((.((((....)))).))..)))))).((....)))))))))). ( -47.20)
>consensus
AAUCGAUGGCAGUGCCGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUCAGCUUCAGCUGCAGCCUUAGCCUGCGAUUGCGAUUGCCGC
(((((..(((.(((((.((((......))))))))).........(((..((((...))))((((((((((((....)))))..))))))).)))...)))..)))))........... (-42.49 = -42.60 +   0.11)

alignment

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secondary structure

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Window 3

Location 21,723,687 – 21,723,806
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.11
Mean single sequence MFE -33.98
Consensus MFE -32.54
Energy contribution -32.14
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -2.30
Structure conservation index 0.96
SVM decision value 4.28
SVM RNA-class probability 0.999859
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21723687 119 + 23771897
GAAGUACCAGCCAACUGCCGAUCAAAUCGAUGCCGUGUAUCGUGUACCUCUCCAUCCUGAGGCG-GCACUGCCAUCGAUUUAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAAC
...(((.(((....)))......((((((((((.((((..((....((((........))))))-)))).).)))))))))...)))......(((((((((.....).))))))))... ( -35.30)
>DroPse_CAF1 32378 112 + 1
--------AGCCAACUGCCGAUCAAAUCGAUGCCGUGUAUCGUGUACCUCUCCAUCCUGAGACGGGCAUCGCCAUCGAUUUAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAAC
--------...........(((.(((((((((.((......((((.((((((......)))).)))))))).))))))))).)))........(((((((((.....).))))))))... ( -33.60)
>DroSec_CAF1 5604 119 + 1
GAAGUACCAGCCAACUGCCGAUCAAAUCGAUGCCGUGUAUCGUGUACCUCUCCAUCCUGAGACG-GCACUGCCAUCGAUUUAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAAC
...(((.(((....)))......((((((((((.((((..(((....(((........))))))-)))).).)))))))))...)))......(((((((((.....).))))))))... ( -33.70)
>DroSim_CAF1 10623 119 + 1
GAAGUACCAGCCAACUGCCGAUCAAAUCGAUGCCGUGUAUCGUGUACCUCUCCAUCCUGAGACG-GCACUGCCAUCGAUUUAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAAC
...(((.(((....)))......((((((((((.((((..(((....(((........))))))-)))).).)))))))))...)))......(((((((((.....).))))))))... ( -33.70)
>DroPer_CAF1 31092 112 + 1
--------AGCCAACUGCCGAUCAAAUCGAUGCCGUGUAUCGUGUACCUCUCCAUCCUGAGACGGGCAUCGCCAUCGAUUUAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAAC
--------...........(((.(((((((((.((......((((.((((((......)))).)))))))).))))))))).)))........(((((((((.....).))))))))... ( -33.60)
>consensus
GAAGUACCAGCCAACUGCCGAUCAAAUCGAUGCCGUGUAUCGUGUACCUCUCCAUCCUGAGACG_GCACUGCCAUCGAUUUAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAAC
...................(((.((((((((((.((((....(((..(((........)))))).)))).).))))))))).)))........(((((((((.....).))))))))... (-32.54 = -32.14 +  -0.40)

alignment

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secondary structure

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Window 4

Location 21,723,687 – 21,723,806
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.11
Mean single sequence MFE -42.76
Consensus MFE -36.36
Energy contribution -36.96
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.85
SVM decision value 2.37
SVM RNA-class probability 0.993027
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21723687 119 - 23771897
GUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUAAAUCGAUGGCAGUGC-CGCCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUC
...((((((((........))))))))......(((((((((((((((.(.((((-(..(((......))).)))))..(.....)).))))))))))))((((.....)))).)))... ( -42.60)
>DroPse_CAF1 32378 112 - 1
GUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUAAAUCGAUGGCGAUGCCCGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCU--------
....(((((((........)))))))(((..((((.((((((((((((.((....(((((....)))))....(((.....))).)).))))))))))))..))))..))).-------- ( -41.70)
>DroSec_CAF1 5604 119 - 1
GUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUAAAUCGAUGGCAGUGC-CGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUC
...((((((((........))))))))......(((((((((((((((.(.((((-(.((((......)))))))))..(.....)).))))))))))))((((.....)))).)))... ( -43.90)
>DroSim_CAF1 10623 119 - 1
GUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUAAAUCGAUGGCAGUGC-CGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUC
...((((((((........))))))))......(((((((((((((((.(.((((-(.((((......)))))))))..(.....)).))))))))))))((((.....)))).)))... ( -43.90)
>DroPer_CAF1 31092 112 - 1
GUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUAAAUCGAUGGCGAUGCCCGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCU--------
....(((((((........)))))))(((..((((.((((((((((((.((....(((((....)))))....(((.....))).)).))))))))))))..))))..))).-------- ( -41.70)
>consensus
GUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUAAAUCGAUGGCAGUGC_CGUCUCAGGAUGGAGAGGUACACGAUACACGGCAUCGAUUUGAUCGGCAGUUGGCUGGUACUUC
....(((((((........)))))))(((..((((.((((((((((((.(.((((.(.((((......)))))))))..(.....)).))))))))))))..))))..)))......... (-36.36 = -36.96 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,723,766 – 21,723,881
Length 115
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 97.40
Mean single sequence MFE -28.04
Consensus MFE -23.73
Energy contribution -24.23
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.85
SVM decision value 0.27
SVM RNA-class probability 0.660104
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21723766 115 + 23771897
UAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAACAUUUGCACACUUUCGAAGCAAAGCAAACAGUUCAACCAGCUGAA-CCGAUCGAAAAACAGGAAAGGGGCCUAAUGC
.............(((((((((.....).))))))))..((((.((...(((((...((...))...(.(((((......))))-).)............)))))..))..)))). ( -27.50)
>DroSec_CAF1 5683 115 + 1
UAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAACAUUUGCACACUUUCGAAGCAAAGCGAACAGUUCAACCAGCUGAA-CCGAUCGAAAAACAGGAAAGGGGCCUAAUGC
.............(((((((((.....).))))))))..((((.((...(((((.........(((.(.(((((......))))-).).)))........)))))..))..)))). ( -30.43)
>DroSim_CAF1 10702 115 + 1
UAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAACAUUUGCACACUUUCGAAGCAAAGCAAACAGUUCAACCAGCUGAA-CCGAUCGAAAAACAGGAAAGGGGCCUAAUGC
.............(((((((((.....).))))))))..((((.((...(((((...((...))...(.(((((......))))-).)............)))))..))..)))). ( -27.50)
>DroYak_CAF1 56287 116 + 1
UAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAACAUUUGCACACUUUCAAAGCAAAGCAAACAGUUCAACCAGCUGAAGCCGAUCGAAAAACAGGAAAGGAGGCUAAAGC
..............((((((((.....).)))))))((((.(((((................)))))..)))).....(((..((((..((.............)).))))..))) ( -26.71)
>consensus
UAAUUACAACAAACGCGUCAGCAAAUUGCCUGACGCGAACAUUUGCACACUUUCGAAGCAAAGCAAACAGUUCAACCAGCUGAA_CCGAUCGAAAAACAGGAAAGGGGCCUAAUGC
.............(((((((((.....).))))))))..((((.((...(((((...((...))...(((((.....)))))..................)))))..))..)))). (-23.73 = -24.23 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,723,766 – 21,723,881
Length 115
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 97.40
Mean single sequence MFE -34.12
Consensus MFE -30.01
Energy contribution -29.82
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.83
Structure conservation index 0.88
SVM decision value 0.09
SVM RNA-class probability 0.577311
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21723766 115 - 23771897
GCAUUAGGCCCCUUUCCUGUUUUUCGAUCGG-UUCAGCUGGUUGAACUGUUUGCUUUGCUUCGAAAGUGUGCAAAUGUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUA
(((((..(((.(((((..((....(((.(((-(((((....)))))))).)))....))...))))).).)).))))).((((((((........))))))))............. ( -33.90)
>DroSec_CAF1 5683 115 - 1
GCAUUAGGCCCCUUUCCUGUUUUUCGAUCGG-UUCAGCUGGUUGAACUGUUCGCUUUGCUUCGAAAGUGUGCAAAUGUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUA
(((((..(((.(((((..((....(((.(((-(((((....)))))))).)))....))...))))).).)).))))).((((((((........))))))))............. ( -36.00)
>DroSim_CAF1 10702 115 - 1
GCAUUAGGCCCCUUUCCUGUUUUUCGAUCGG-UUCAGCUGGUUGAACUGUUUGCUUUGCUUCGAAAGUGUGCAAAUGUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUA
(((((..(((.(((((..((....(((.(((-(((((....)))))))).)))....))...))))).).)).))))).((((((((........))))))))............. ( -33.90)
>DroYak_CAF1 56287 116 - 1
GCUUUAGCCUCCUUUCCUGUUUUUCGAUCGGCUUCAGCUGGUUGAACUGUUUGCUUUGCUUUGAAAGUGUGCAAAUGUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUA
((....))...(((((......((((((((((....))))))))))......((...))...)))))..(((((.....((((((((........))))))))....))))).... ( -32.70)
>consensus
GCAUUAGGCCCCUUUCCUGUUUUUCGAUCGG_UUCAGCUGGUUGAACUGUUUGCUUUGCUUCGAAAGUGUGCAAAUGUUCGCGUCAGGCAAUUUGCUGACGCGUUUGUUGUAAUUA
...........(((((..((....(((.(((.(((((....)))))))).)))....))...)))))..(((((.....((((((((........))))))))....))))).... (-30.01 = -29.82 +  -0.19)

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 13:11:02 2006