Locus 5607

Sequence ID X_DroMel_CAF1
Location 14,468,550 – 14,468,806
Length 256
Max. P 0.971993
window9104 window9105 window9106 window9107 window9108

overview

Window 4

Location 14,468,550 – 14,468,663
Length 113
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.77
Mean single sequence MFE -38.90
Consensus MFE -35.47
Energy contribution -35.37
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.98
Structure conservation index 0.91
SVM decision value 1.68
SVM RNA-class probability 0.971993
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14468550 113 - 22224390
ACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGUGGAGAUGGAGGUCCCAACUCGAUGGCUUUCCCAAUUCCACAGCUCACA-------GAUU
........(((((((((...(((((.((....)).)))))...)))))))...))((((.(((((.(((..(..(((......)))..)..))).))))))))).....-------.... ( -35.30)
>DroSim_CAF1 5237 113 - 1
ACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGUGGAGAUGGAGGGCCCAACUCGAUGGCUUUCCCAAUCCCACAGCUCACA-------GAUU
........(((((((((...(((((.((....)).)))))...)))))))...))((((..(((...((((((((.........))))))))...)))..)))).....-------.... ( -38.00)
>DroYak_CAF1 1753 120 - 1
ACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGCGGAGAUGGAGAGCCCAACUCGAUGGCUUUCCCAAUCCCACAGCUCACAGCUCACGGAUU
.(((((..(((((((((...(((((.((....)).)))))...)))))))...))..))))).....((((((((.........)))))))).(((((...(((.....)))...))))) ( -43.40)
>consensus
ACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGUGGAGAUGGAGGGCCCAACUCGAUGGCUUUCCCAAUCCCACAGCUCACA_______GAUU
........(((((((((...(((((.((....)).)))))...)))))))...))((((..(((...((((((((.........))))))))...)))..))))................ (-35.47 = -35.37 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,468,583 – 14,468,703
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -38.63
Consensus MFE -35.69
Energy contribution -35.80
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.06
Structure conservation index 0.92
SVM decision value 0.61
SVM RNA-class probability 0.799914
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14468583 120 + 22224390
AGUUGGGACCUCCAUCUCCACCAGCGCUUAACAAUCACUUAGCGCAUUAUUAAAAACGCUUUUUGAUUGCGCUUUGGCGUGUUGGCCCAUUGAAAUCGAUAGGCGUUGCCCGGUGGAUCU
.....((....))...((((((.(((((............))))).........(((((((.((((((...(..(((.((....)))))..).)))))).)))))))....))))))... ( -38.20)
>DroSim_CAF1 5270 120 + 1
AGUUGGGCCCUCCAUCUCCACCAGCGCUUAACAAUCACUUAGCGCAUUAUUAAAAACGCUUUUUGAUUGCGCUUUGGCGUGUUGGCCCAUUGAAAUCGAUAGGCGUUGCCCGGUGGAUCU
.(.(((.....))).)((((((.(((((............))))).........(((((((.((((((...(..(((.((....)))))..).)))))).)))))))....))))))... ( -38.10)
>DroYak_CAF1 1793 120 + 1
AGUUGGGCUCUCCAUCUCCGCCAGCGCUUAACAAUCACUUAGCGCAUUAUUAAAAACGCUUUUUGAUUGCGCUUUGGCGUGUUGGCCCAUUGAAAUCGAUAGGCGUAGCCCAGUGGAUCU
..((((((((.((......((((((((....((((((...((((............))))...)))))).((....))))))))))..((((....)))).)).).)))))))....... ( -39.60)
>consensus
AGUUGGGCCCUCCAUCUCCACCAGCGCUUAACAAUCACUUAGCGCAUUAUUAAAAACGCUUUUUGAUUGCGCUUUGGCGUGUUGGCCCAUUGAAAUCGAUAGGCGUUGCCCGGUGGAUCU
.(.(((.....))).)((((((.(.((.(((((....(..((((((..(((((((.....)))))))))))))..)...)))))(((.((((....)))).)))...))).))))))... (-35.69 = -35.80 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,468,583 – 14,468,703
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -41.67
Consensus MFE -38.45
Energy contribution -38.57
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -3.01
Structure conservation index 0.92
SVM decision value 1.60
SVM RNA-class probability 0.966504
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14468583 120 - 22224390
AGAUCCACCGGGCAACGCCUAUCGAUUUCAAUGGGCCAACACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGUGGAGAUGGAGGUCCCAACU
...((((((((((...((((((.(....).))))))......((....))(((((((...(((((.((....)).)))))...)))))))...)).))))))))..(((.....)))... ( -40.80)
>DroSim_CAF1 5270 120 - 1
AGAUCCACCGGGCAACGCCUAUCGAUUUCAAUGGGCCAACACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGUGGAGAUGGAGGGCCCAACU
...((((((((((...((((((.(....).))))))......((....))(((((((...(((((.((....)).)))))...)))))))...)).))))))))..(((.....)))... ( -40.80)
>DroYak_CAF1 1793 120 - 1
AGAUCCACUGGGCUACGCCUAUCGAUUUCAAUGGGCCAACACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGCGGAGAUGGAGAGCCCAACU
........((((((..((((((.(....).)))))).....(((((..(((((((((...(((((.((....)).)))))...)))))))...))..))))).........))))))... ( -43.40)
>consensus
AGAUCCACCGGGCAACGCCUAUCGAUUUCAAUGGGCCAACACGCCAAAGCGCAAUCAAAAAGCGUUUUUAAUAAUGCGCUAAGUGAUUGUUAAGCGCUGGUGGAGAUGGAGGGCCCAACU
.........((((...((((((.(....).)))))).....(((((..(((((((((...(((((.((....)).)))))...)))))))...))..)))))..........)))).... (-38.45 = -38.57 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,468,703 – 14,468,806
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -23.67
Consensus MFE -15.42
Energy contribution -15.76
Covariance contribution 0.34
Combinations/Pair 1.09
Mean z-score -1.36
Structure conservation index 0.65
SVM decision value 0.13
SVM RNA-class probability 0.595779
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14468703 103 + 22224390
UGGCCAGCGGCUUAGCAUUAGAUACCCUAACUGCGAAGAUCUUGACAGGGUAUCGUAUUAUUUUCAACCAAUACAAAUACAU------------UGUAAGUUAAGAUAAUACUU-----A
.((((...))))........((((((((.....(((.....)))..))))))))((((((((((.(((...(((((.....)------------)))).)))))))))))))..-----. ( -25.40)
>DroSim_CAF1 5390 114 + 1
UGGCCAGCGGCUUAGCAUUAGAUACCCUAACUGCGGAGAUCUUGACAGGGUAUCGUAUUAUUUU-AAGUAAUAAAAAUACAUGUUACUUCAAGGUCUAAGUUAAAAUAAUACCA-----A
.((((...))))........((((((((..(...((....)).)..))))))))((((((((((-((((((((........))))))).............)))))))))))..-----. ( -24.71)
>DroYak_CAF1 1913 116 + 1
UGGCCAGCGGCUGAGCGUUAGAUACCCUAGCUCCACAGAUCUUGACAGGGUAUCAUAGUAUUUC-AAUCUAUAAAAAUAUAUCGUACUUAAAC---GAAAUUAAAAUAGUUUCAUCGGAA
.((((...))))(((((.((((((((((..(............)..))))))))((((......-...)))).......)).)))........---(((((((...))))))).)).... ( -20.90)
>consensus
UGGCCAGCGGCUUAGCAUUAGAUACCCUAACUGCGAAGAUCUUGACAGGGUAUCGUAUUAUUUU_AACCAAUAAAAAUACAU__UACUU_AA__U_UAAGUUAAAAUAAUACCA_____A
.((((...))))........((((((((..(............)..))))))))((((((((((......................................))))))))))........ (-15.42 = -15.76 +   0.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,468,703 – 14,468,806
Length 103
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.22
Mean single sequence MFE -24.77
Consensus MFE -17.01
Energy contribution -17.24
Covariance contribution 0.23
Combinations/Pair 1.15
Mean z-score -1.39
Structure conservation index 0.69
SVM decision value 0.52
SVM RNA-class probability 0.767753
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14468703 103 - 22224390
U-----AAGUAUUAUCUUAACUUACA------------AUGUAUUUGUAUUGGUUGAAAAUAAUACGAUACCCUGUCAAGAUCUUCGCAGUUAGGGUAUCUAAUGCUAAGCCGCUGGCCA
.-----..(((((((.((((((((((------------(.....)))))..))))))..)))))))(((((((((....(.....).....)))))))))....((((......)))).. ( -27.00)
>DroSim_CAF1 5390 114 - 1
U-----UGGUAUUAUUUUAACUUAGACCUUGAAGUAACAUGUAUUUUUAUUACUU-AAAAUAAUACGAUACCCUGUCAAGAUCUCCGCAGUUAGGGUAUCUAAUGCUAAGCCGCUGGCCA
.-----..(((((((((((((((........)))).....(((.......))).)-))))))))))(((((((((....(.....).....)))))))))....((((......)))).. ( -24.80)
>DroYak_CAF1 1913 116 - 1
UUCCGAUGAAACUAUUUUAAUUUC---GUUUAAGUACGAUAUAUUUUUAUAGAUU-GAAAUACUAUGAUACCCUGUCAAGAUCUGUGGAGCUAGGGUAUCUAACGCUCAGCCGCUGGCCA
......(((...((((((((((((---((......))))((((....))))))))-))))))....(((((((((......((....))..)))))))))......)))(((...))).. ( -22.50)
>consensus
U_____UGGUAUUAUUUUAACUUA_A__UU_AAGUA__AUGUAUUUUUAUUGAUU_AAAAUAAUACGAUACCCUGUCAAGAUCUCCGCAGUUAGGGUAUCUAAUGCUAAGCCGCUGGCCA
........((((((((((((((.............................)))).))))))))))(((((((((................))))))))).........(((...))).. (-17.01 = -17.24 +   0.23)

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 11:52:10 2006