Locus 4069

Sequence ID 2L_DroMel_CAF1
Location 11,750,438 – 11,750,737
Length 299
Max. P 0.999971
window6411 window6412 window6413

overview

Window 1

Location 11,750,438 – 11,750,548
Length 110
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 93.44
Mean single sequence MFE -34.12
Consensus MFE -32.32
Energy contribution -32.16
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.77
Structure conservation index 0.95
SVM decision value 5.05
SVM RNA-class probability 0.999971
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11750438 110 + 22407834
UGCCACCUCGAGUCAUCCUUUUAAUUAUGUAACACGCGCCACCACAGGAGUGUUGCCUUACGCACUUCGGUCUUCGGUCUGCGGUCCUUUUUGGUGGCAAACAUUU-------UCCA
(((((((..(((................(((((((...((......)).)))))))....((((..(((.....)))..))))...)))...))))))).......-------.... ( -32.50)
>DroSec_CAF1 8760 110 + 1
UGCCACCUCGAGCCAUCCUUUUAAUUAUGUAACACGCGCCACCACAGGAGUGUUGCCUUACGCACUUCGGUCUUCGGUCUGCGGUCCUUUUUGGUGGCAAAAAUUU-------UCCA
(((((((..(..((..............(((((((...((......)).))))))).....(((..(((.....)))..)))))..).....))))))).......-------.... ( -32.60)
>DroSim_CAF1 7630 110 + 1
UGCCACCUCGAGCCAUCCUUUUAAUUAUGUAACACGCGCCACCACAGGAGUGUUGCCUUACGCACUUCGGUCUUCGGUCUGCGGUCCUUUUUGGUGGCAAACAUUU-------UCCA
(((((((..(..((..............(((((((...((......)).))))))).....(((..(((.....)))..)))))..).....))))))).......-------.... ( -32.60)
>DroEre_CAF1 15897 117 + 1
UGCCACCUCAAGCCAUCUUUUUAAUUAUGUAACACGCGCCACCACUGGAGUGUUGCCUUACGCACUUCGGUCUUCGGUCUGCGGCUCUUUUUGGUGGCAAACAUUUUCCAUUUUCCA
(((((((...((((..............(((((((...(((....))).))))))).....(((..(((.....)))..)))))))......))))))).................. ( -35.80)
>DroYak_CAF1 9157 109 + 1
UGCCACCUCGAGCCAUCUUUUUAAUUAUGUAACACGCGCCGCCACUGGAGUGUUGCCUUACGCACUUCGGUCUUCGGUCUGCGGUUCUUUUUGGUGGCAAACAUA--------UCCA
(((((((..(((((..............(.....)((((((..((((((((((........))))))))))...))))..))))))).....)))))))......--------.... ( -37.10)
>consensus
UGCCACCUCGAGCCAUCCUUUUAAUUAUGUAACACGCGCCACCACAGGAGUGUUGCCUUACGCACUUCGGUCUUCGGUCUGCGGUCCUUUUUGGUGGCAAACAUUU_______UCCA
(((((((..(((................(((((((...((......)).)))))))....((((..(((.....)))..))))...)))...))))))).................. (-32.32 = -32.16 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,750,515 – 11,750,619
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 92.56
Mean single sequence MFE -28.04
Consensus MFE -24.45
Energy contribution -24.27
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.20
Structure conservation index 0.87
SVM decision value 1.38
SVM RNA-class probability 0.948198
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11750515 104 - 22407834
AAGAACACGCAACUACUGGCCAACGGAAGUGUGGAAUAUGCCCAGUGGGGGGAAAAAUGUUGGCAGGAAAAUGGAAAAUGUUUGCCACCAAAAAGGACCGCAGA
........((..((((((((((((....)).))).......)))))))((.......((.(((((((...((.....)).))))))).)).......))))... ( -27.65)
>DroSec_CAF1 8837 102 - 1
AAGAACACGCAACUACUGGCCAACGGAAGUGUGGAAUAUGCCCAGUGGGGGG--AAAUGUUGGCAGGAAAAUGGAAAAUUUUUGCCACCAAAAAGGACCGCAGA
........((..((((((((((((....)).))).......))))))).((.--......(((((((((.........)))))))))((.....)).))))... ( -28.41)
>DroSim_CAF1 7707 102 - 1
AAGAACACGCAACUACUGGCCAACGGAAGUGUGGAAUAUGCCCAGUGGGGGA--AAAUGUUGGCAGGAAAAUGGAAAAUGUUUGCCACCAAAAAGGACCGCAGA
........((..((((((((((((....)).))).......)))))))((..--......(((((((...((.....)).)))))))((.....)).))))... ( -27.31)
>DroYak_CAF1 9234 100 - 1
AAGGACACGCAACUACUGGCCAACGGAAGUGCUGAAAAUGCUCAGUGGGG-A--AAGUGGUGGCAGGAAAAUGGA-UAUGUUUGCCACCAAAAAGAACCGCAGA
........((..(((((((...((....))((.......)))))))))((-.--...((((((((((...((...-.)).)))))))))).......))))... ( -28.80)
>consensus
AAGAACACGCAACUACUGGCCAACGGAAGUGUGGAAUAUGCCCAGUGGGGGA__AAAUGUUGGCAGGAAAAUGGAAAAUGUUUGCCACCAAAAAGGACCGCAGA
........((..(((((((.((((....))........)).)))))))((.......((.(((((((...((.....)).))))))).)).......))))... (-24.45 = -24.27 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,750,619 – 11,750,737
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 85.43
Mean single sequence MFE -25.18
Consensus MFE -19.06
Energy contribution -17.75
Covariance contribution -1.31
Combinations/Pair 1.26
Mean z-score -1.39
Structure conservation index 0.76
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11750619 118 + 22407834
CAAGUGUGAACUUAAUUCAGAUAAAGCGAAAAUUCUGAUAAGUUUAAUUGCUAUCCUAAAUGGUGACAAAGCGUUUGCAUUUAUAUUCAUGUAUACACAUACACAUGAAUAGCCGUAG
.(((((..(((.....(((((............)))))...((((..(..((((.....))))..)..)))))))..))))).(((((((((.((....)).)))))))))....... ( -27.10)
>DroSim_CAF1 7809 118 + 1
CACGUGUGAACUUAAUUCAGAUAAAGCGAAAAUUCUGAUAAGUUUAAUUGCUAGCCUAAAUGGUGACAAAGCGUUAGCGCUUAUUUUUAUGUAUACACAUACACAUGAAUAGCCGUAG
.(((..((((((((..(((((............)))))))))))))...((((((((...((....)).)).))))))(((.((((...(((((....)))))...)))))))))).. ( -27.90)
>DroEre_CAF1 16082 110 + 1
CACGUGUGAACUUAAUUCAGAUAAAGCGAAAACUCUGAUAAGUUUAAUUGUUGGCCUAAAUGGUGACAAAGCGUUUGCACUUAUUUUCAGGGAUA--------UUUGAAUAGCCAUAG
.(((..((((((((..(((((............)))))))))))))..)))((((......((((.(((.....)))))))....((((((....--------))))))..))))... ( -20.90)
>DroYak_CAF1 9334 110 + 1
CACGUGUGAACUUUAUUCAGAUAAAGCGAAAAUUCUGAUAAGUUUAAUUGCUAUCCUAAAUGGUGACAAAGCGUUUGCACUUGCUUUCAUGGGAU--------UAUGAAUAGCCACAG
...(((..(((.....(((((............)))))...((((..(..((((.....))))..)..)))))))..)))..(((((((((....--------)))))).)))..... ( -24.80)
>consensus
CACGUGUGAACUUAAUUCAGAUAAAGCGAAAAUUCUGAUAAGUUUAAUUGCUAGCCUAAAUGGUGACAAAGCGUUUGCACUUAUUUUCAUGGAUA________CAUGAAUAGCCAUAG
...((((((((.....(((((............)))))...((((..(..(((.......)))..)..)))))))))))).....((((((............))))))......... (-19.06 = -17.75 +  -1.31)

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 11:08:34 2006