Locus 5415

Sequence ID X_DroMel_CAF1
Location 14,107,610 – 14,107,748
Length 138
Max. P 0.994215
window8781 window8782 window8783 window8784

overview

Window 1

Location 14,107,610 – 14,107,709
Length 99
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 82.51
Mean single sequence MFE -32.63
Consensus MFE -22.02
Energy contribution -22.47
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -4.29
Structure conservation index 0.67
SVM decision value 2.36
SVM RNA-class probability 0.992962
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14107610 99 + 22224390
UAGAGUUU--------------ACAGAUUAGAGUUUAGAGUUUAGAGCUUAUAGCU------CUAAAGAUUUGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCGAAAGCUCUUGACCUU
.(((((((--------------.(......((((((.(((((((((((.....)))------)))..))))).))))))..(((((((((....)))))))))).)))))))....... ( -33.10)
>DroSec_CAF1 18150 105 + 1
UAGAAUUU--------------AGAGAUUAGAGUUUAGAGUUUAGAGUUUAGAGCUAAGAGCUUACAGAUUAGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCAAAAGCUCUUGACCUU
........--------------.(((.(((((((((.((((((..(((((.((((.....))))..)))))..))))))..(((((((((....)))))))))..)))))).))).))) ( -29.40)
>DroSim_CAF1 18631 119 + 1
UAGAGUUUAGAGUUUAGAGUUUAGAGAUUAGAGUUUAUAGUUUAGAGUCUAGAGCUAAGAGCUUACAGAUUAGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCAAAAGCUCUUGACCUU
.((.(((.(((((((.((((((...((((.((((((.((((((........)))))).))))))...))))..))))))..(((((((((....)))))))))..))))))).))))). ( -35.40)
>consensus
UAGAGUUU______________AGAGAUUAGAGUUUAGAGUUUAGAGUUUAGAGCUAAGAGCUUACAGAUUAGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCAAAAGCUCUUGACCUU
.............................((.(((.(((((((.((((((....((..........)).....))))))..(((((((((....)))))))))..))))))).))))). (-22.02 = -22.47 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,107,610 – 14,107,709
Length 99
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 82.51
Mean single sequence MFE -23.27
Consensus MFE -17.52
Energy contribution -17.63
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -4.42
Structure conservation index 0.75
SVM decision value 2.46
SVM RNA-class probability 0.994215
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14107610 99 - 22224390
AAGGUCAAGAGCUUUCGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCAAAUCUUUAG------AGCUAUAAGCUCUAAACUCUAAACUCUAAUCUGU--------------AAACUCUA
.((((..((((.....(((((((((....)))))))))..............(((((------(((.....))))))))))))..)).)).......--------------........ ( -25.50)
>DroSec_CAF1 18150 105 - 1
AAGGUCAAGAGCUUUUGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCUAAUCUGUAAGCUCUUAGCUCUAAACUCUAAACUCUAAACUCUAAUCUCU--------------AAAUUCUA
.(((..((((((((..(((((((((....)))))))))..((........))...))))))))..).))............................--------------........ ( -21.80)
>DroSim_CAF1 18631 119 - 1
AAGGUCAAGAGCUUUUGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCUAAUCUGUAAGCUCUUAGCUCUAGACUCUAAACUAUAAACUCUAAUCUCUAAACUCUAAACUCUAAACUCUA
.(((((.((((((...(((((((((....)))))))))..((........))...........)))))).))).))........................................... ( -22.50)
>consensus
AAGGUCAAGAGCUUUUGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCUAAUCUGUAAGCUCUUAGCUCUAAACUCUAAACUCUAAACUCUAAUCUCU______________AAACUCUA
.((((..((((((...(((((((((....)))))))))..((........))...........))))))..)).))........................................... (-17.52 = -17.63 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,107,636 – 14,107,748
Length 112
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 81.46
Mean single sequence MFE -30.98
Consensus MFE -17.16
Energy contribution -17.80
Covariance contribution 0.64
Combinations/Pair 1.12
Mean z-score -2.57
Structure conservation index 0.55
SVM decision value 1.20
SVM RNA-class probability 0.929829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14107636 112 + 22224390
UUUAGAGCUUAUAGCU------CUAAAGAUUUGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCGAAAGCUCUUGACCUUCUAUCGUCAUAGUCUUAGUCU-UGUCUCUUGUCUCAAUUG
((((((((.....)))------)))))(((..(((((..(((((((((((....)))))))))..(((((..((((........)))).)).)))..)).-.)))))..)))....... ( -35.90)
>DroSec_CAF1 18176 118 + 1
UUUAGAGUUUAGAGCUAAGAGCUUACAGAUUAGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCAAAAGCUCUUGACCUUCUAUCGUCAUAGUCUUAGUCU-UGUCUCUUGUCUCAAUUG
....(((...((((.(((((.((...(((((((((......(((((((((....))))))))).....))).((((........)))))))))).)))))-)).))))...)))..... ( -33.90)
>DroSim_CAF1 18671 118 + 1
UUUAGAGUCUAGAGCUAAGAGCUUACAGAUUAGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCAAAAGCUCUUGACCUUCUAUCGUCAUAGUCUUAGUCU-UGUCUCUUGUCUCAAUUG
....(((.(.((((.(((((.((...(((((((((......(((((((((....))))))))).....))).((((........)))))))))).)))))-)).)))).).)))..... ( -34.80)
>DroEre_CAF1 19572 112 + 1
-----AGCGUAGAGCUUAGAGCCUAGACCUUAUAGAUUAGAGAUGGUAGCAGUUGCUAUGAUCUA-AGCCCUCGACCAUCUAUCGCCAUAGUCUUAGUCU-UGUCUCUUGUCUCAAUUG
-----......(((...((((.(.((((.....((((((.(((((((.(.((..(((........-))).))).))))))).......))))))..))))-.).))))...)))..... ( -26.80)
>DroYak_CAF1 17809 108 + 1
-----AGCGUAGAGCUUAGU-----GAGCUUAUAGAUAAGAGAUUAUGGCAAUUGCUAUAAUCGA-AGCCCUUGAACAUCUUUCGACACCGUCUUAGUCUUUGUCUCUCGUCUCAAUUG
-----.(((.(((((..((.-----..(((...((((....(((((((((....)))))))))..-.....(((((.....)))))....)))).)))))..).)))))))........ ( -23.50)
>consensus
UUUAGAGCGUAGAGCUAAGAGCCUACAGAUUAGAGAUUCGAGAUUAUAGCAGUUGCUAUAAUCAAAAGCUCUUGACCUUCUAUCGUCAUAGUCUUAGUCU_UGUCUCUUGUCUCAAUUG
.....(((.....)))................(((((..(((((((((((....)))))))))..........(((...((((....)))).....)))......))..)))))..... (-17.16 = -17.80 +   0.64)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,107,636 – 14,107,748
Length 112
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 81.46
Mean single sequence MFE -29.02
Consensus MFE -16.36
Energy contribution -17.92
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.66
Structure conservation index 0.56
SVM decision value 1.40
SVM RNA-class probability 0.950749
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14107636 112 - 22224390
CAAUUGAGACAAGAGACA-AGACUAAGACUAUGACGAUAGAAGGUCAAGAGCUUUCGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCAAAUCUUUAG------AGCUAUAAGCUCUAAA
...((((((...((....-....................((((((.....))))))(((((((((....)))))))))))...))))))....((((------(((.....))))))). ( -32.20)
>DroSec_CAF1 18176 118 - 1
CAAUUGAGACAAGAGACA-AGACUAAGACUAUGACGAUAGAAGGUCAAGAGCUUUUGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCUAAUCUGUAAGCUCUUAGCUCUAAACUCUAAA
...........((((...-(((((((((((.((((........))))((((.(((.(((((((((....)))))))))..))).))))........)).)))))).)))...))))... ( -31.30)
>DroSim_CAF1 18671 118 - 1
CAAUUGAGACAAGAGACA-AGACUAAGACUAUGACGAUAGAAGGUCAAGAGCUUUUGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCUAAUCUGUAAGCUCUUAGCUCUAGACUCUAAA
...........((((.(.-(((((((((((.((((........))))((((.(((.(((((((((....)))))))))..))).))))........)).)))))).))).).))))... ( -32.10)
>DroEre_CAF1 19572 112 - 1
CAAUUGAGACAAGAGACA-AGACUAAGACUAUGGCGAUAGAUGGUCGAGGGCU-UAGAUCAUAGCAACUGCUACCAUCUCUAAUCUAUAAGGUCUAGGCUCUAAGCUCUACGCU-----
...........((((.(.-.......((((((........)))))).((((((-((((((.((((....)))).......((.....)).))))))))))))..))))).....----- ( -27.90)
>DroYak_CAF1 17809 108 - 1
CAAUUGAGACGAGAGACAAAGACUAAGACGGUGUCGAAAGAUGUUCAAGGGCU-UCGAUUAUAGCAAUUGCCAUAAUCUCUUAUCUAUAAGCUC-----ACUAAGCUCUACGCU-----
......((.((((((.(.........((..(..((....))..)))..(((((-(.((((((.((....)).))))))..........))))))-----.....))))).))))----- ( -21.60)
>consensus
CAAUUGAGACAAGAGACA_AGACUAAGACUAUGACGAUAGAAGGUCAAGAGCUUUCGAUUAUAGCAACUGCUAUAAUCUCGAAUCUCUAAUCUCUAAGCUCUAAGCUCUAAGCUCUAAA
.....(((...((((.(...((((....((((....))))..)))).(((......(((((((((....))))))))).....)))..................)))))...))).... (-16.36 = -17.92 +   1.56)

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 11:47:22 2006