Locus 7162

Sequence ID 2L_DroMel_CAF1
Location 20,042,645 – 20,042,871
Length 226
Max. P 0.988784
window11432 window11433 window11434 window11435 window11436

overview

Window 2

Location 20,042,645 – 20,042,762
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 84.01
Mean single sequence MFE -34.97
Consensus MFE -25.68
Energy contribution -25.47
Covariance contribution -0.21
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.73
SVM decision value 0.16
SVM RNA-class probability 0.613599
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20042645 117 - 22407834
UGGGUUGAGGGUUGAGGGUUUCGGGGUUUUCUCCGGAAAACUGUUCACUUCAGUUCUUGCCACUCAGUGGUGGCAAGCGUGAAAUUGAAAUUUAUGCUCUAAUUACAAACGAAUGCC
.(..(((((((...((..((((((((....))))))))..))...).))))))..)((((((((....))))))))(((((((.......))))))).................... ( -37.80)
>DroSec_CAF1 224929 107 - 1
UGGGUCG-------AGGGUUUCGGGGUUUUCCCCGGAAAACUCG---GAAAACUGUUUGCUACUCAGUGGUGGCAAGCGUGAAAUUGAAAUUUAUGCUCUAAUUACAAACGAAUGCC
.((((((-------((..((((((((....))))))))..))))---.......((((((((((....)))))))))).................)))).................. ( -36.80)
>DroEre_CAF1 219805 108 - 1
UGGGUCG-------AGGGCUACGGGGUUUUCCCCGGAAAACUGUUCACUUCAG--UUCGCUACUCAGUGGUGGCAAGCGUGAAAUUGAAAUUUAUGCUCUAAUUACAAAUGAAUGCC
..(((.(-------(((....(((((....)))))(((.....))).)))).(--(((((((((....)))))).((((((((.......))))))))............))))))) ( -30.30)
>consensus
UGGGUCG_______AGGGUUUCGGGGUUUUCCCCGGAAAACUGUUCACUUCAGU_UUUGCUACUCAGUGGUGGCAAGCGUGAAAUUGAAAUUUAUGCUCUAAUUACAAACGAAUGCC
.((.(((.......((..((((((((....))))))))..))................((((((....)))))).((((((((.......))))))))...........)))...)) (-25.68 = -25.47 +  -0.21)

alignment

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secondary structure

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Window 3

Location 20,042,685 – 20,042,800
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 81.95
Mean single sequence MFE -34.17
Consensus MFE -22.85
Energy contribution -23.63
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.82
Structure conservation index 0.67
SVM decision value 1.64
SVM RNA-class probability 0.969440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20042685 115 + 22407834
CUUGCCACCACUGAGUGGCAAGAACUGAAGUGAACAGUUUUCCGGAGAAAACCCCGAAACCCUCAACCCUCAACCCACAAGCCCCAUUGUGGGGCAACAUUUAACACUUGGCAUG
((((((((......)))))))).....(((((....((((((....)))))).....................(((((((......)))))))...........)))))...... ( -32.80)
>DroSec_CAF1 224969 105 + 1
CUUGCCACCACUGAGUAGCAAACAGUUUUC---CGAGUUUUCCGGGGAAAACCCCGAAACCCU-------CGACCCACAAGCCCCAUUGUGGGGCUACAUUUAACACUUGGCAUG
..(((((.....(((((((...........---((((..((.(((((....))))).))..))-------)).(((((((......)))))))))))).)).......))))).. ( -39.20)
>DroEre_CAF1 219845 106 + 1
CUUGCCACCACUGAGUAGCGAA--CUGAAGUGAACAGUUUUCCGGGGAAAACCCCGUAGCCCU-------CGACCCACAAGCCCCAAAGUUGGGCAACAUUUAACACUUGGCAUG
..(((((....((((..(((((--(((.......))))))..(((((....)))))..)).))-------))........((((.......)))).............))))).. ( -30.50)
>consensus
CUUGCCACCACUGAGUAGCAAA_ACUGAAGUGAACAGUUUUCCGGGGAAAACCCCGAAACCCU_______CGACCCACAAGCCCCAUUGUGGGGCAACAUUUAACACUUGGCAUG
..(((((....(((((....................((((..(((((....)))))))))....................(((((.....)))))...))))).....))))).. (-22.85 = -23.63 +   0.78)

alignment

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secondary structure

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Window 4

Location 20,042,685 – 20,042,800
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 81.95
Mean single sequence MFE -40.61
Consensus MFE -29.41
Energy contribution -29.97
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.72
SVM decision value 0.90
SVM RNA-class probability 0.876942
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20042685 115 - 22407834
CAUGCCAAGUGUUAAAUGUUGCCCCACAAUGGGGCUUGUGGGUUGAGGGUUGAGGGUUUCGGGGUUUUCUCCGGAAAACUGUUCACUUCAGUUCUUGCCACUCAGUGGUGGCAAG
..((((..............(((((.....)))))....(..(((((((...((..((((((((....))))))))..))...).))))))..)..(((((...))))))))).. ( -43.30)
>DroSec_CAF1 224969 105 - 1
CAUGCCAAGUGUUAAAUGUAGCCCCACAAUGGGGCUUGUGGGUCG-------AGGGUUUCGGGGUUUUCCCCGGAAAACUCG---GAAAACUGUUUGCUACUCAGUGGUGGCAAG
..(((((..........((((((((((((......)))))))(((-------((..((((((((....))))))))..))))---)..........))))).......))))).. ( -44.83)
>DroEre_CAF1 219845 106 - 1
CAUGCCAAGUGUUAAAUGUUGCCCAACUUUGGGGCUUGUGGGUCG-------AGGGCUACGGGGUUUUCCCCGGAAAACUGUUCACUUCAG--UUCGCUACUCAGUGGUGGCAAG
..(((((.............((((.......))))...(((((.(-------.(((((.(((((....)))))(((.....))).....))--))).).)))))....))))).. ( -33.70)
>consensus
CAUGCCAAGUGUUAAAUGUUGCCCCACAAUGGGGCUUGUGGGUCG_______AGGGUUUCGGGGUUUUCCCCGGAAAACUGUUCACUUCAGU_UUUGCUACUCAGUGGUGGCAAG
..((((..............(((((.....))))).................((..((((((((....))))))))..))................(((((...))))))))).. (-29.41 = -29.97 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,042,722 – 20,042,840
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 89.63
Mean single sequence MFE -35.80
Consensus MFE -33.43
Energy contribution -34.10
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.93
SVM decision value 2.13
SVM RNA-class probability 0.988784
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20042722 118 + 22407834
UUUUCCGGAGAAAACCCCGAAACCCUCAACCCUCAACCCACAAGCCCCAUUGUGGGGCAACAUUUAACACUUGGCAUGGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCCACCA
.....(((........))).................(((((((......)))))))...............(((((((((.((((.....)))))))(((.....))).))))))... ( -33.30)
>DroSec_CAF1 225003 111 + 1
UUUUCCGGGGAAAACCCCGAAACCCU-------CGACCCACAAGCCCCAUUGUGGGGCUACAUUUAACACUUGGCAUGGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCCACCA
.....(((((....))))).......-------.........((((((.....))))))............(((((((((.((((.....)))))))(((.....))).))))))... ( -40.20)
>DroEre_CAF1 219880 108 + 1
UUUUCCGGGGAAAACCCCGUAGCCCU-------CGACCCACAAGCCCCAAAGUUGGGCAACAUUUAACACUUGGCAUGGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCC---A
.....(((((....))))).......-------..........((((.......)))).............(((((((((.((((.....)))))))(((.....))).)))))---) ( -33.90)
>consensus
UUUUCCGGGGAAAACCCCGAAACCCU_______CGACCCACAAGCCCCAUUGUGGGGCAACAUUUAACACUUGGCAUGGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCCACCA
.....(((((....)))))........................(((((.....)))))..............((((((((.((((.....)))))))(((.....))).))))).... (-33.43 = -34.10 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,042,762 – 20,042,871
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.23
Mean single sequence MFE -29.00
Consensus MFE -9.92
Energy contribution -11.88
Covariance contribution 1.96
Combinations/Pair 1.23
Mean z-score -2.27
Structure conservation index 0.34
SVM decision value 1.26
SVM RNA-class probability 0.937711
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20042762 109 + 22407834
CAAGCCCCAUUGUGGGGCAACAUUUAACACUUGGCAU--GGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCCACCAAAUGAACAACAAACAACG--AGCGGAG---CAACAA----
...(((((.....)))))..(((((......((((((--(((.((((.....)))))))(((.....))).))))))..)))))..............--.......---......---- ( -31.00)
>DroSec_CAF1 225036 109 + 1
CAAGCCCCAUUGUGGGGCUACAUUUAACACUUGGCAU--GGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCCACCAAAUUAACAACAAACAACG--AGCGGAG---CAACAA----
..((((((.....))))))..........(((.((.(--(((.((((.....))))))))......(((((((........)))))))..........--.)).)))---......---- ( -35.00)
>DroEre_CAF1 219913 103 + 1
CAAGCCCCAAAGUUGGGCAACAUUUAACACUUGGCAU--GGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCC---AAGUGAA---CAAACAACG--AGCAGAG---CAACAA----
...((((.......)))).........((((((((((--(((.((((.....)))))))(((.....))).)))))---)))))..---.........--.......---......---- ( -34.40)
>DroYak_CAF1 218957 96 + 1
-------CAUCGUUGGGCAACAUUUAACACUUGGCAU--GGGAGCGUAGCACGUGCCCCAACAUUAUGGUACUGCG---AAAUGAA---CAAACAACG--AGCAAAG---UAACAA----
-------..(((((((....)......((.((.((((--(((.(((.....)))..))))((......))..))).---)).))..---....)))))--)......---......---- ( -21.60)
>DroAna_CAF1 234988 109 + 1
-----UUCAUUGUGUGGCAACAUUUAGAAUUUAAUACUGAGAAGAGUAGCACGUGCCCAGACAUUAUGUUAAUGCC---AAAUGAA---CAAACAACAGAGGCAGAGGCGCCACCAGGAG
-----.((.(((.(((((................((((......))))......((((.(((.....)))..((((---...((..---.......))..))))).))))))))))))). ( -23.00)
>consensus
CAAGCCCCAUUGUGGGGCAACAUUUAACACUUGGCAU__GGGAGCGCAGCACGUGCCCCAACAUUAUGUUAAUGCC___AAAUGAA___CAAACAACG__AGCAGAG___CAACAA____
...(((((.....)))))...........(((.((....(((.((((.....)))))))..(((((...)))))...........................)).)))............. ( -9.92 = -11.88 +   1.96)

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 12:29:00 2006