Locus 2472

Sequence ID 3L_DroMel_CAF1
Location 6,974,612 – 6,974,766
Length 154
Max. P 0.843066
window3813 window3814 window3815

overview

Window 3

Location 6,974,612 – 6,974,726
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.35
Mean single sequence MFE -30.16
Consensus MFE -23.75
Energy contribution -24.91
Covariance contribution 1.16
Combinations/Pair 1.09
Mean z-score -1.74
Structure conservation index 0.79
SVM decision value 0.52
SVM RNA-class probability 0.768563
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6974612 114 + 23771897
GGGGCUAGUCAAUAAGUCAACUUAUUCGCCUGCGAAUUUCGCGAUUUAUGGGGCCCAGCUUUAUAUAU------AAAUACAUACCUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGA
.(((((.....(((((((.....(((((....))))).....)))))))..))))).((((((..(((------......)))..)))))).((((((((((.....)))))..))))). ( -33.70)
>DroSec_CAF1 44546 120 + 1
GGGGCUAGUCAAUAAGUCAACUUAUUCGCCUGCGAAUUUCGCGAUUUAUGGGGCUCAGCUUUAUAUAUACAUAUAUAUACGUACUUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGA
.(((((.....(((((((.....(((((....))))).....)))))))..))))).((((((((((((....))))))......)))))).((((((((((.....)))))..))))). ( -30.80)
>DroSim_CAF1 44307 120 + 1
GGGGCUAGUCAAUAAGUCAACUUAUUCGCCUGCGAAUUUCGCGAUUUAUGGGGCUCAGCUUUAUAUAUGCAUAUAUAUACGUACUUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGA
.(((((.....(((((((.....(((((....))))).....)))))))..))))).((((((..((((.((....)).))))..)))))).((((((((((.....)))))..))))). ( -33.20)
>DroEre_CAF1 44496 109 + 1
GG-GCUAGUCAAUAAGUCAACUUAUUUGCCUGAGAACUUUGCGAUUUGUGGGGCUCAGCUUUAUAUAU----------GCGAAUUUAAAGCGCGAUAAUUGCACAUUGCAAACAUGUCGA
((-((.....((((((....)))))).))))((.(..((((((((.((..(...((.((((((.((..----------....)).))))))..))...)..)).))))))))..).)).. ( -27.20)
>DroYak_CAF1 45863 110 + 1
GGGGCUAGUCAAUAAGUCAACUUAUUCGUCUGAGAACUUCGCGAUUUAUGGGGCUCAGCUUUAUAUAU----------GUGAGUUUAAUACGCGAUAAUUGCAUAUUGCAAUCAUGUCGA
...(((((.(((((((....)))))).).))).(((((.((((...((((((((...))))))))..)----------)))))))).....))(((((((((.....)))))..)))).. ( -25.90)
>consensus
GGGGCUAGUCAAUAAGUCAACUUAUUCGCCUGCGAAUUUCGCGAUUUAUGGGGCUCAGCUUUAUAUAU______A_AUACGUACUUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGA
.(((((.....(((((((.....(((((....))))).....)))))))..))))).((((((......................)))))).((((((((((.....)))))..))))). (-23.75 = -24.91 +   1.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,974,652 – 6,974,766
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.73
Mean single sequence MFE -25.97
Consensus MFE -22.09
Energy contribution -22.53
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.57
Structure conservation index 0.85
SVM decision value 0.76
SVM RNA-class probability 0.843066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6974652 114 + 23771897
GCGAUUUAUGGGGCCCAGCUUUAUAUAU------AAAUACAUACCUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGAAAUAAACUUGUAAUUAUUGCAUAUAAAUCUUGAGUGAGAG
..((((((((.......((((((..(((------......)))..))))))((((((((((((..((....((.....))....))..)))))))))))).))))))))........... ( -26.00)
>DroSec_CAF1 44586 120 + 1
GCGAUUUAUGGGGCUCAGCUUUAUAUAUACAUAUAUAUACGUACUUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGAAAUAAACUUGUAAUUAUUGCAUAUAAAUCUUGAGUGAGAG
..((((((((.......((((((((((((....))))))......))))))((((((((((((..((....((.....))....))..)))))))))))).))))))))........... ( -26.10)
>DroSim_CAF1 44347 120 + 1
GCGAUUUAUGGGGCUCAGCUUUAUAUAUGCAUAUAUAUACGUACUUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGAAAUAAACUUGUAAUUAUUGCAUAUAAAUCUUGAGUGAGAG
..((((((((.......((((((..((((.((....)).))))..))))))((((((((((((..((....((.....))....))..)))))))))))).))))))))........... ( -28.50)
>DroEre_CAF1 44535 110 + 1
GCGAUUUGUGGGGCUCAGCUUUAUAUAU----------GCGAAUUUAAAGCGCGAUAAUUGCACAUUGCAAACAUGUCGAAAUAAACUUGUAAUUAUUGCAUAUAAAUCUUGAGUGAGAG
..((((((((.......((((((.((..----------....)).))))))((((((((((((..((.................))..)))))))))))).))))))))........... ( -23.43)
>DroYak_CAF1 45903 110 + 1
GCGAUUUAUGGGGCUCAGCUUUAUAUAU----------GUGAGUUUAAUACGCGAUAAUUGCAUAUUGCAAUCAUGUCGAAAUAAACUUGUAAUUAUUGCAUAUAAAUCUUGAGUGAGAG
(((((.((((((((...))))))))..(----------(..((((((.....((((((((((.....)))))..)))))...))))))..))...))))).......((((....)))). ( -25.80)
>consensus
GCGAUUUAUGGGGCUCAGCUUUAUAUAU______A_AUACGUACUUAAAGCGCGAUAAUUGCAUAUUGCAAUCAUGUCGAAAUAAACUUGUAAUUAUUGCAUAUAAAUCUUGAGUGAGAG
..((((((((.......((((((......................))))))((((((((((((..((....((.....))....))..)))))))))))).))))))))........... (-22.09 = -22.53 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,974,652 – 6,974,766
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.73
Mean single sequence MFE -21.85
Consensus MFE -16.13
Energy contribution -16.57
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.74
SVM decision value 0.44
SVM RNA-class probability 0.739156
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6974652 114 - 23771897
CUCUCACUCAAGAUUUAUAUGCAAUAAUUACAAGUUUAUUUCGACAUGAUUGCAAUAUGCAAUUAUCGCGCUUUAGGUAUGUAUUU------AUAUAUAAAGCUGGGCCCCAUAAAUCGC
...........(((((((..((...........(((......)))((((((((.....)))))))).))((((((.(((((....)------)))).))))))........))))))).. ( -23.80)
>DroSec_CAF1 44586 120 - 1
CUCUCACUCAAGAUUUAUAUGCAAUAAUUACAAGUUUAUUUCGACAUGAUUGCAAUAUGCAAUUAUCGCGCUUUAAGUACGUAUAUAUAUGUAUAUAUAAAGCUGAGCCCCAUAAAUCGC
...........(((((((..((...........(((......)))((((((((.....)))))))).))((((((.(((((((....)))))))...))))))........))))))).. ( -24.80)
>DroSim_CAF1 44347 120 - 1
CUCUCACUCAAGAUUUAUAUGCAAUAAUUACAAGUUUAUUUCGACAUGAUUGCAAUAUGCAAUUAUCGCGCUUUAAGUACGUAUAUAUAUGCAUAUAUAAAGCUGAGCCCCAUAAAUCGC
...........(((((((..((...........(((......)))((((((((.....)))))))).))((((((.(((.((((....)))).))).))))))........))))))).. ( -24.60)
>DroEre_CAF1 44535 110 - 1
CUCUCACUCAAGAUUUAUAUGCAAUAAUUACAAGUUUAUUUCGACAUGUUUGCAAUGUGCAAUUAUCGCGCUUUAAAUUCGC----------AUAUAUAAAGCUGAGCCCCACAAAUCGC
...........(((((...(((((.....(((.(((......))).))))))))..(((......(((.((((((.((....----------..)).)))))))))....)))))))).. ( -17.00)
>DroYak_CAF1 45903 110 - 1
CUCUCACUCAAGAUUUAUAUGCAAUAAUUACAAGUUUAUUUCGACAUGAUUGCAAUAUGCAAUUAUCGCGUAUUAAACUCAC----------AUAUAUAAAGCUGAGCCCCAUAAAUCGC
......((((...((((((((...........((((((...((..((((((((.....))))))))..))...))))))...----------.))))))))..))))............. ( -19.06)
>consensus
CUCUCACUCAAGAUUUAUAUGCAAUAAUUACAAGUUUAUUUCGACAUGAUUGCAAUAUGCAAUUAUCGCGCUUUAAGUACGUAU_U______AUAUAUAAAGCUGAGCCCCAUAAAUCGC
...........(((((((..((...........(((......)))((((((((.....)))))))).))((((((......................))))))........))))))).. (-16.13 = -16.57 +   0.44)

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 10:33:10 2006