Locus 176

Sequence ID 3R_DroMel_CAF1
Location 837,977 – 838,128
Length 151
Max. P 0.976015
window293 window294 window295 window296

overview

Window 3

Location 837,977 – 838,093
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.22
Mean single sequence MFE -35.92
Consensus MFE -33.10
Energy contribution -33.60
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.92
SVM decision value 0.36
SVM RNA-class probability 0.704245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 837977 116 + 27905053
GACUGAAUCUGCCGCAGCGCAUAAUGUGUAAGCACUCAUAUUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGG---CGAGUGCUUUGCGUCACCG-
.........((.((((((((.....))))((((((((..........((((......))))...(((((((........)))))))...........---.)))))))))))).))...- ( -35.40)
>DroSec_CAF1 13456 119 + 1
GACUGAAUCUGCCGCAGCGCAUAAUGUGUAAGCACUCAUAUUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGGCGGCGAGUGCUUUGCGUCACCG-
.........((.((((((((.....))))(((((((((((....)))..((..(((........(((((((........)))))))........)))..)))))))))))))).))...- ( -35.79)
>DroSim_CAF1 12948 119 + 1
GACUGAAUCUGCCGCAGCGCAUAAUGUGUAAGCACUCAUAUUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGGCGGCGAGUGCUUUGCGUCACCG-
.........((.((((((((.....))))(((((((((((....)))..((..(((........(((((((........)))))))........)))..)))))))))))))).))...- ( -35.79)
>DroEre_CAF1 15097 117 + 1
GACUGAAUCUGCCGCAGAGCAUAAUGUGUAAGCACUCGUAUUUAUAUUCGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGG---UGAGUGCUUUGCGUCACCGA
....((((.(((((.(((((..((((((...((....))...)))))).))))))).)))))))(((((((........))))))).......((((---(((.(((...)))))))))) ( -36.70)
>consensus
GACUGAAUCUGCCGCAGCGCAUAAUGUGUAAGCACUCAUAUUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGG___CGAGUGCUUUGCGUCACCG_
.........((.((((((((.....))))((((((((..........((((......))))...(((((((........)))))))...............)))))))))))).)).... (-33.10 = -33.60 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 837,977 – 838,093
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.22
Mean single sequence MFE -34.15
Consensus MFE -31.48
Energy contribution -31.35
Covariance contribution -0.13
Combinations/Pair 1.03
Mean z-score -1.48
Structure conservation index 0.92
SVM decision value -0.02
SVM RNA-class probability 0.521232
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 837977 116 - 27905053
-CGGUGACGCAAAGCACUCG---CCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAAUAUGAGUGCUUACACAUUAUGCGCUGCGGCAGAUUCAGUC
-((....))..........(---(((((((.(..(((((((........))))))).....((((....................))))..........).)))).)))).......... ( -32.15)
>DroSec_CAF1 13456 119 - 1
-CGGUGACGCAAAGCACUCGCCGCCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAAUAUGAGUGCUUACACAUUAUGCGCUGCGGCAGAUUCAGUC
-.(((((.((...))..)))))((((((((.(..(((((((........))))))).....((((....................))))..........).)))).)))).......... ( -35.85)
>DroSim_CAF1 12948 119 - 1
-CGGUGACGCAAAGCACUCGCCGCCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAAUAUGAGUGCUUACACAUUAUGCGCUGCGGCAGAUUCAGUC
-.(((((.((...))..)))))((((((((.(..(((((((........))))))).....((((....................))))..........).)))).)))).......... ( -35.85)
>DroEre_CAF1 15097 117 - 1
UCGGUGACGCAAAGCACUCA---CCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACGAAUAUAAAUACGAGUGCUUACACAUUAUGCUCUGCGGCAGAUUCAGUC
(((((((.((...))..)))---))))(((....(((((((........))))))).....((((....................))))...)))....((((....))))......... ( -32.75)
>consensus
_CGGUGACGCAAAGCACUCG___CCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAAUAUGAGUGCUUACACAUUAUGCGCUGCGGCAGAUUCAGUC
.((....)).....(((((......)))))(((.(((((((........)))))))...((((.((....((.((....)).))(((((...........))))).)))))).))).... (-31.48 = -31.35 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 838,017 – 838,128
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.41
Mean single sequence MFE -30.55
Consensus MFE -25.14
Energy contribution -24.95
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -2.65
Structure conservation index 0.82
SVM decision value 1.65
SVM RNA-class probability 0.969900
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 838017 111 + 27905053
UUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGG---CGAGUGCUUUGCGUCACCG------GACGUUUGUAAUCACCAUUUUUACAUAUAUUCUAC
...((((.(((....(((.((...(((((((........))))))).)).)))..((---.((.(((...(((((....------)))))..))).)).))......))).))))..... ( -30.40)
>DroSec_CAF1 13496 114 + 1
UUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGGCGGCGAGUGCUUUGCGUCACCG------GACGUUCGUAAUCACCAUUUAUACACAUAUUCUAC
...((((.(((....(((.((...(((((((........))))))).)).))).....((.((.(((...(((((....------)))))..))).)).))......))).))))..... ( -29.50)
>DroSim_CAF1 12988 114 + 1
UUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGGCGGCGAGUGCUUUGCGUCACCG------GACGUUCGUAAUCACCAUUUAUACACAUAUUCUAC
...((((.(((....(((.((...(((((((........))))))).)).))).....((.((.(((...(((((....------)))))..))).)).))......))).))))..... ( -29.50)
>DroEre_CAF1 15137 113 + 1
UUUAUAUUCGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGG---UGAGUGCUUUGCGUCACCGAUUAUGGACGUUCAUAAUCGCCAUUU----AAAUAUUCCAC
.((((...(((((..(((.((...(((((((........))))))).)).)))((((---(((.(((...))))))))))....)))))...)))).........----........... ( -32.80)
>consensus
UUUAUAUUUGUUCUCGUGCAAUUUGCAGCCAUACAAUGUUGGCUGCUUUCCACUCGG___CGAGUGCUUUGCGUCACCG______GACGUUCGUAAUCACCAUUUAUACACAUAUUCUAC
.................((((...(((((((........)))))))....((((((....))))))..))))(((..........)))................................ (-25.14 = -24.95 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 838,017 – 838,128
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.41
Mean single sequence MFE -30.80
Consensus MFE -27.48
Energy contribution -27.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.89
SVM decision value 1.76
SVM RNA-class probability 0.976015
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 838017 111 - 27905053
GUAGAAUAUAUGUAAAAAUGGUGAUUACAAACGUC------CGGUGACGCAAAGCACUCG---CCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAA
.....((((.(((.......(..(((.....((..------((((((.((...))..)))---)))..))....(((((((........))))))).)))..)......))).))))... ( -29.02)
>DroSec_CAF1 13496 114 - 1
GUAGAAUAUGUGUAUAAAUGGUGAUUACGAACGUC------CGGUGACGCAAAGCACUCGCCGCCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAA
.....((((.(((......((((........)).)------)(....)((((..((((((....))))))....(((((((........)))))))...))))......))).))))... ( -29.70)
>DroSim_CAF1 12988 114 - 1
GUAGAAUAUGUGUAUAAAUGGUGAUUACGAACGUC------CGGUGACGCAAAGCACUCGCCGCCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAA
.....((((.(((......((((........)).)------)(....)((((..((((((....))))))....(((((((........)))))))...))))......))).))))... ( -29.70)
>DroEre_CAF1 15137 113 - 1
GUGGAAUAUUU----AAAUGGCGAUUAUGAACGUCCAUAAUCGGUGACGCAAAGCACUCA---CCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACGAAUAUAAA
.....((((((----...((((((((.......(((((..(((((((.((...))..)))---)))))))))..(((((((........))))))).)))))).)).....))))))... ( -34.80)
>consensus
GUAGAAUAUGUGUAUAAAUGGUGAUUACGAACGUC______CGGUGACGCAAAGCACUCG___CCGAGUGGAAAGCAGCCAACAUUGUAUGGCUGCAAAUUGCACGAGAACAAAUAUAAA
...............................(((........(....)((((..(((((......)))))....(((((((........)))))))...))))))).............. (-27.48 = -27.47 +  -0.00)

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 09:36:01 2006