Locus 6077

Sequence ID 3L_DroMel_CAF1
Location 16,156,997 – 16,157,270
Length 273
Max. P 0.901966
window9757 window9758 window9759 window9760 window9761 window9762 window9763

overview

Window 7

Location 16,156,997 – 16,157,112
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.94
Mean single sequence MFE -30.88
Consensus MFE -22.20
Energy contribution -22.57
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -1.84
Structure conservation index 0.72
SVM decision value 0.39
SVM RNA-class probability 0.716602
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16156997 115 + 23771897
UA-----UUCCUACAUUUAGCACUUAAGCGGCAACUACUGUAUAUUCAUAGCUCGUUUUAAGCCUGUGAUUCAGAUUUAGAUUGAGUUACGGCUUCCCGUAGUCGUCGGCUCUGGUGCUC
..-----...........((((((..((((((.(((((..........(((((((.(((((..(((.....)))..))))).))))))).((....))))))).))).)))..)))))). ( -35.00)
>DroSec_CAF1 14513 115 + 1
UA-----UUCCCACAUUUAGCAUUUAAGCAGCAAAUACUGUAUAUUCAUAGCUCGAUUUAAACCUGUGAUUCAGAUUUAGAUUGAGAUACGGCUUUCCGUAGUCGUCGGCUCUGGUGCUC
..-----...........((((((..(((......................(((((((((((.(((.....))).)))))))))))..((((((......))))))..)))..)))))). ( -29.90)
>DroSim_CAF1 15827 115 + 1
UA-----UUAUCACAUUUAGCAUUUAAGCGACCACUACUGUAUAUUCAUAGCUCGUUUUAAGCCUGUGAUUCAGAUUUAGAUUGAGAUACGGCUUUCCGUAGUCGUCGGCUGUGGUGCUC
..-----...........((((((..((((((.(((((.............((((.(((((..(((.....)))..))))).))))....((....))))))).))).)))..)))))). ( -28.40)
>DroEre_CAF1 13883 120 + 1
UACGCACCUCCAAGAUUUAGCAUUUAAACCGCAACUACUGUAUAUUCAUGCCCCGUUGUAAGUCUGUGAUUCAGAUUUAGAUUGAGAUACGGCUUUCCAUAGUCGUCGGCUCUGGUGCUC
...(((((.....((((((...........(((((....((((....))))...))))).((((((.....))))))))))))(((..((((((......))))))...))).))))).. ( -30.20)
>consensus
UA_____UUCCCACAUUUAGCAUUUAAGCGGCAACUACUGUAUAUUCAUAGCUCGUUUUAAGCCUGUGAUUCAGAUUUAGAUUGAGAUACGGCUUUCCGUAGUCGUCGGCUCUGGUGCUC
..................((((((..(((......................((((.((((((.(((.....))).)))))).))))..((((((......))))))..)))..)))))). (-22.20 = -22.57 +   0.37)

alignment

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secondary structure

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Window 8

Location 16,156,997 – 16,157,112
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.94
Mean single sequence MFE -29.39
Consensus MFE -21.27
Energy contribution -21.34
Covariance contribution 0.06
Combinations/Pair 1.17
Mean z-score -1.66
Structure conservation index 0.72
SVM decision value 0.22
SVM RNA-class probability 0.637852
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16156997 115 - 23771897
GAGCACCAGAGCCGACGACUACGGGAAGCCGUAACUCAAUCUAAAUCUGAAUCACAGGCUUAAAACGAGCUAUGAAUAUACAGUAGUUGCCGCUUAAGUGCUAAAUGUAGGAA-----UA
.(((((..((((.(.(((((((((....))(((.(((....(((..(((.....)))..)))....))).))).........)))))))).))))..)))))...........-----.. ( -31.20)
>DroSec_CAF1 14513 115 - 1
GAGCACCAGAGCCGACGACUACGGAAAGCCGUAUCUCAAUCUAAAUCUGAAUCACAGGUUUAAAUCGAGCUAUGAAUAUACAGUAUUUGCUGCUUAAAUGCUAAAUGUGGGAA-----UA
.((((.((.((((((.((.(((((....)))))))......((((((((.....))))))))..))).))).))..((..((((....))))..))..))))...........-----.. ( -26.10)
>DroSim_CAF1 15827 115 - 1
GAGCACCACAGCCGACGACUACGGAAAGCCGUAUCUCAAUCUAAAUCUGAAUCACAGGCUUAAAACGAGCUAUGAAUAUACAGUAGUGGUCGCUUAAAUGCUAAAUGUGAUAA-----UA
.((((....(((.(((.(((((((....))((((.(((........(((.....)))((((.....))))..)))..)))).))))).))))))....))))...........-----.. ( -27.50)
>DroEre_CAF1 13883 120 - 1
GAGCACCAGAGCCGACGACUAUGGAAAGCCGUAUCUCAAUCUAAAUCUGAAUCACAGACUUACAACGGGGCAUGAAUAUACAGUAGUUGCGGUUUAAAUGCUAAAUCUUGGAGGUGCGUA
..(((((.((((((.(((((((.......(((..(((....(((.((((.....)))).)))....)))..)))........))))))))))))).....(((.....))).)))))... ( -32.76)
>consensus
GAGCACCAGAGCCGACGACUACGGAAAGCCGUAUCUCAAUCUAAAUCUGAAUCACAGGCUUAAAACGAGCUAUGAAUAUACAGUAGUUGCCGCUUAAAUGCUAAAUGUGGGAA_____UA
.((((...((((.(.(((((((.......((((.(((....(((.((((.....)))).)))....))).))))........)))))))).))))...)))).................. (-21.27 = -21.34 +   0.06)

alignment

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secondary structure

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Window 9

Location 16,157,072 – 16,157,192
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -29.25
Consensus MFE -28.58
Energy contribution -28.57
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.98
SVM decision value 0.64
SVM RNA-class probability 0.808571
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16157072 120 + 23771897
AUUGAGUUACGGCUUCCCGUAGUCGUCGGCUCUGGUGCUCACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAA
...(((((((((((......)))))).)))))(((((..((......((((...(((((..((((.....))))...)))))...))))...))..)))))((((((......)))))). ( -30.20)
>DroSec_CAF1 14588 120 + 1
AUUGAGAUACGGCUUUCCGUAGUCGUCGGCUCUGGUGCUCACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAA
((((((..((((((......)))))).(((......)))..))))))((((...(((((..((((.....))))...)))))...)))).(((((..(((....)))..)))))...... ( -28.70)
>DroSim_CAF1 15902 120 + 1
AUUGAGAUACGGCUUUCCGUAGUCGUCGGCUGUGGUGCUCACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAA
((((((....(((...(((((((.....))))))).)))..))))))((((...(((((..((((.....))))...)))))...)))).(((((..(((....)))..)))))...... ( -29.40)
>DroEre_CAF1 13963 120 + 1
AUUGAGAUACGGCUUUCCAUAGUCGUCGGCUCUGGUGCUCACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAA
((((((....(((...(((.(((.....))).))).)))..))))))((((...(((((..((((.....))))...)))))...)))).(((((..(((....)))..)))))...... ( -28.70)
>consensus
AUUGAGAUACGGCUUUCCGUAGUCGUCGGCUCUGGUGCUCACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAA
((((((..((((((......)))))).(((......)))..))))))((((...(((((..((((.....))))...)))))...)))).(((((..(((....)))..)))))...... (-28.58 = -28.57 +  -0.00)

alignment

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secondary structure

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Window 0

Location 16,157,072 – 16,157,192
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -30.45
Consensus MFE -30.29
Energy contribution -30.10
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.14
Structure conservation index 0.99
SVM decision value 0.98
SVM RNA-class probability 0.894382
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16157072 120 - 23771897
UUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGUGAGCACCAGAGCCGACGACUACGGGAAGCCGUAACUCAAU
......(((((.((((....)))).))))).((((((.(((((.(((..........))).))))).))))))((((((((.((......)))......(((((....)))))))))))) ( -33.60)
>DroSec_CAF1 14588 120 - 1
UUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGUGAGCACCAGAGCCGACGACUACGGAAAGCCGUAUCUCAAU
......(((((.((((....)))).))))).((((((.(((((.(((..........))).))))).))))))((((((((.((......)))).....(((((....))))).)))))) ( -30.00)
>DroSim_CAF1 15902 120 - 1
UUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGUGAGCACCACAGCCGACGACUACGGAAAGCCGUAUCUCAAU
......(((((.((((....)))).))))).((((((.(((((.(((..........))).))))).))))))((((((((.((......)))).....(((((....))))).)))))) ( -30.00)
>DroEre_CAF1 13963 120 - 1
UUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGUGAGCACCAGAGCCGACGACUAUGGAAAGCCGUAUCUCAAU
......(((((.((((....)))).))))).((((((.(((((.(((..........))).))))).))))))((((((((.((......)))).....(((((....))))).)))))) ( -28.20)
>consensus
UUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGUGAGCACCAGAGCCGACGACUACGGAAAGCCGUAUCUCAAU
......(((((.((((....)))).))))).((((((.(((((.(((..........))).))))).))))))((((((((.((......)))).....(((((....))))).)))))) (-30.29 = -30.10 +  -0.19)

alignment

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secondary structure

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Window 1

Location 16,157,112 – 16,157,232
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -34.00
Consensus MFE -34.00
Energy contribution -34.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.69
Structure conservation index 1.00
SVM decision value 1.02
SVM RNA-class probability 0.901966
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16157112 120 + 23771897
ACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAACUGCCAGACAAACUGGCAGGCAGUGGCGCAGACAGACAGC
.......((((...(((((..((((.....))))...)))))...))))..((((.(((((((((((......)))))..(((((((.....)))))))...))))))...))))..... ( -34.00)
>DroSec_CAF1 14628 120 + 1
ACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAACUGCCAGACAAACUGGCAGGCAGUGGCGCAGACAGACAGC
.......((((...(((((..((((.....))))...)))))...))))..((((.(((((((((((......)))))..(((((((.....)))))))...))))))...))))..... ( -34.00)
>DroSim_CAF1 15942 120 + 1
ACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAACUGCCAGACAAACUGGCAGGCAGUGGCGCAGACAGACAGC
.......((((...(((((..((((.....))))...)))))...))))..((((.(((((((((((......)))))..(((((((.....)))))))...))))))...))))..... ( -34.00)
>DroEre_CAF1 14003 120 + 1
ACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAACUGCCAGACAAACUGGCAGGCAGUGGCGCAGACAGACAGC
.......((((...(((((..((((.....))))...)))))...))))..((((.(((((((((((......)))))..(((((((.....)))))))...))))))...))))..... ( -34.00)
>consensus
ACUCAAUUAUUCAGGCAUAAUAAGCAAAUUGUUUUAAUAUGCAUAAAUAUCUUGUACGCCAUUUGGCAAACAAGUCAAAACUGCCAGACAAACUGGCAGGCAGUGGCGCAGACAGACAGC
.......((((...(((((..((((.....))))...)))))...))))..((((.(((((((((((......)))))..(((((((.....)))))))...))))))...))))..... (-34.00 = -34.00 +   0.00)

alignment

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secondary structure

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Window 2

Location 16,157,112 – 16,157,232
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -33.00
Consensus MFE -33.00
Energy contribution -33.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 1.00
SVM decision value 0.49
SVM RNA-class probability 0.755066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16157112 120 - 23771897
GCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGU
(((.(((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))((((((.(((((.(((..........))).))))).))))))....))) ( -33.00)
>DroSec_CAF1 14628 120 - 1
GCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGU
(((.(((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))((((((.(((((.(((..........))).))))).))))))....))) ( -33.00)
>DroSim_CAF1 15942 120 - 1
GCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGU
(((.(((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))((((((.(((((.(((..........))).))))).))))))....))) ( -33.00)
>DroEre_CAF1 14003 120 - 1
GCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGU
(((.(((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))((((((.(((((.(((..........))).))))).))))))....))) ( -33.00)
>consensus
GCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGCAUAUUAAAACAAUUUGCUUAUUAUGCCUGAAUAAUUGAGU
(((.(((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))((((((.(((((.(((..........))).))))).))))))....))) (-33.00 = -33.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,157,152 – 16,157,270
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.59
Mean single sequence MFE -30.30
Consensus MFE -29.20
Energy contribution -29.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.96
SVM decision value 0.72
SVM RNA-class probability 0.831517
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16157152 118 - 23771897
GUAACCCCCCUUUCCACAACACCCCCCC--CCCCCCUGCAGCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGC
............................--.......(((..(((((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))))....))) ( -29.20)
>DroSec_CAF1 14668 117 - 1
GUAAGUCCCCUUUCCA-ACCAACCCCCU--CCCCCCUGCAGCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGC
((((((..........-..(((......--.......(((((.....).))))........(((((((.....)))))))..))).(((((.((((....)))).)))))..)))))).. ( -29.70)
>DroSim_CAF1 15982 119 - 1
GUAAGCCCCCUUUCGA-ACCAACCCCCUUCCCCCCCUGCAGCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGC
(((((.......((((-(...................(((((.....).))))........(((((((.....))))))).)))))(((((.((((....)))).)))))...))))).. ( -30.60)
>DroEre_CAF1 14043 102 - 1
----GGCCCCUUUCG------------C--CCCCCCUGCAGCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGC
----(((.......)------------)--)......(((..(((((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))))....))) ( -31.70)
>consensus
GUAAGCCCCCUUUCCA_ACCAACCCCCC__CCCCCCUGCAGCUGUCUGUCUGCGCCACUGCCUGCCAGUUUGUCUGGCAGUUUUGACUUGUUUGCCAAAUGGCGUACAAGAUAUUUAUGC
.....................................(((..(((((...(((((((....(((((((.....))))))).((((.(......).)))))))))))..)))))....))) (-29.20 = -29.20 +  -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 12:09:26 2006