Locus 782

Sequence ID 2R_DroMel_CAF1
Location 3,746,115 – 3,746,425
Length 310
Max. P 0.980357
window1369 window1370 window1371 window1372

overview

Window 9

Location 3,746,115 – 3,746,235
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.25
Mean single sequence MFE -34.50
Consensus MFE -30.79
Energy contribution -30.79
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.89
SVM decision value 0.02
SVM RNA-class probability 0.543309
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3746115 120 + 20766785
UGCUGCUGUGGCUUCUCCUCUUUCUUUCUUUCCUUUUUUUUCUUAUUCCCGGCCCAGGGAUCAAGGUAAACGCCAUUUAGUGUGGCACGAUCGCUGACGAUCGGUAGCCAGGCUUGUAUC
(((.(((.(((((...((......................((((..((((......))))..)))).....(((((.....)))))..(((((....))))))).))))))))..))).. ( -35.50)
>DroSim_CAF1 8917 119 + 1
UGCUGCUGUGGCUUCUCCUCUUUCUUUCCUUCCUUUUUUCU-UUAUUCCCGGCCCAGGGAUCAAGGUAAACGCCAUUUAGUGUGGCACGAUCGCUGCCGAUCGGUAGCCAGGCUUGUAUC
(((.(((.(((((...((.................(((.((-((..((((......))))..)))).))).(((((.....)))))..(((((....))))))).))))))))..))).. ( -34.80)
>DroYak_CAF1 8653 112 + 1
U---GCUGUGGCUUCUCUUCGCUCUUU----CCUUUUUUCU-UCAUUCCCGGCUCAGGGAUCAAGGUAAACGCCAUUAAGUGUGGCACGAUCGCUGCCGAUCGGUAGCCAGGCCUGUAUC
(---((...(((((....(((......----.......(((-(...((((......))))..)))).....(((((.....))))).)))..((((((....)))))).))))).))).. ( -33.20)
>consensus
UGCUGCUGUGGCUUCUCCUCUUUCUUUC_UUCCUUUUUUCU_UUAUUCCCGGCCCAGGGAUCAAGGUAAACGCCAUUUAGUGUGGCACGAUCGCUGCCGAUCGGUAGCCAGGCUUGUAUC
....(((.(((((.(................((((...........((((......))))..)))).....(((((.....))))).((((((....))))))).))))))))....... (-30.79 = -30.79 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,746,235 – 3,746,329
Length 94
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.95
Mean single sequence MFE -34.03
Consensus MFE -26.05
Energy contribution -25.83
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.70
Structure conservation index 0.77
SVM decision value 1.86
SVM RNA-class probability 0.980357
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3746235 94 - 20766785
AAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGAAACGACGCACCGAGGAUCCGAGCCCGGGAAGCCCCAAAAAGGAGGA------------------------CUG--ACAGAUACA
.......((((((...........((((((((((....))))))).)))((.(((...((.(((....))).....)).)))------------------------)).--..)))))). ( -28.10)
>DroSim_CAF1 9036 118 - 1
AAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGGAACGACGCACCGAGGAUCCGAGCCCGGGAAGCCCCAAAAAGGAGGACCGGCAGACACAGUACACAUCGUACUG--ACAGAUACA
.......((((((....((((...((((((((((....))))))).)))........(((.((....((((.....)).)).)))))..))))(((((.....))))).--..)))))). ( -38.40)
>DroYak_CAF1 8765 111 - 1
AAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGGAACGACGCACCGAGGAUCCCAGCCCGGGAAGCCCCAAAAAGGAGGACUGGCAGAC---------ACAGUACAGAUACAAAUACA
.......((((((...(((((...((((((((((....))))))).))).....((((.((((....))((.....)).)).))))...))---------)))....))))))....... ( -35.60)
>consensus
AAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGGAACGACGCACCGAGGAUCCGAGCCCGGGAAGCCCCAAAAAGGAGGAC_GGCAGAC_________A__GUACUG__ACAGAUACA
.......((((((...........((((((((((....))))))).)))...(((...((.(((....))).....)).)))...............................)))))). (-26.05 = -25.83 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,746,249 – 3,746,355
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.17
Mean single sequence MFE -36.10
Consensus MFE -31.90
Energy contribution -31.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.88
SVM decision value 0.96
SVM RNA-class probability 0.890972
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3746249 106 - 20766785
UCCCAA--------------CCGACCGGGUGUACAAUAAAAAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGAAACGACGCACCGAGGAUCCGAGCCCGGGAAGCCCCAAAAAGGAG
(((...--------------......((((.((((...(((((......)))))....))))..((((((((((....))))))).)))........))))(((....))).....))). ( -32.90)
>DroSim_CAF1 9074 106 - 1
UCCCAG--------------CCGACCGGGUGUACAAUAAAAAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGGAACGACGCACCGAGGAUCCGAGCCCGGGAAGCCCCAAAAAGGAG
.....(--------------(...((((((.((((...(((((......)))))....))))..((((((((((....))))))).)))........))))))...)).((.....)).. ( -32.30)
>DroYak_CAF1 8796 120 - 1
UCCCAGCUUCGUAUGUACACCCGACCGGGUGUACAAUAAAAAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGGAACGACGCACCGAGGAUCCCAGCCCGGGAAGCCCCAAAAAGGAG
(((...(((((..(((((((((....)))))))))...............................((((((((....))))))))))))).((((.....))))...........))). ( -43.10)
>consensus
UCCCAG______________CCGACCGGGUGUACAAUAAAAAUUAAAGUGUUUUAAUGUGUAAAUCGUGCGUUGGGAACGACGCACCGAGGAUCCGAGCCCGGGAAGCCCCAAAAAGGAG
(((.......................((((.((((...(((((......)))))....))))..((((((((((....))))))).)))........))))(((....))).....))). (-31.90 = -31.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,746,329 – 3,746,425
Length 96
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.93
Mean single sequence MFE -32.92
Consensus MFE -22.85
Energy contribution -22.63
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.07
Structure conservation index 0.69
SVM decision value 0.35
SVM RNA-class probability 0.698328
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3746329 96 - 20766785
AGUCUGCCGGUGC----------CCUCAGAAUUGAUUAAAAAAGAGGGAAGUAGAUCGUCACUGGUCGACAGAUCGAAGCUCCCAA--------------CCGACCGGGUGUACAAUAAA
.(((.((((((((----------((((................)))))...........))))))).)))........((.(((..--------------......))).))........ ( -25.39)
>DroSim_CAF1 9154 96 - 1
AGUCCGCCGGUGC----------CCUCAGAAUUGAUUAAAAAAGAGGGAAGUAGAUCGUCACUGGUCGACAGAUCGAAGCUCCCAG--------------CCGACCGGGUGUACAAUAAA
.(((.((((((((----------((((................)))))...........))))))).)))........((.(((..--------------......))).))........ ( -25.39)
>DroYak_CAF1 8876 120 - 1
AGUCCGCCGGUGUCUUUACUCUGCCUCAGAAUUGAUUAAAAAAGAGGGAAGUAGAUCGUCACUGGUCGACAGAUCGAAGCUCCCAGCUUCGUAUGUACACCCGACCGGGUGUACAAUAAA
.(((.(((((((.(((((((.(.((((................)))).)))))))..).))))))).)))....((((((.....))))))..(((((((((....)))))))))..... ( -47.99)
>consensus
AGUCCGCCGGUGC__________CCUCAGAAUUGAUUAAAAAAGAGGGAAGUAGAUCGUCACUGGUCGACAGAUCGAAGCUCCCAG______________CCGACCGGGUGUACAAUAAA
.((.(((((((..............((......))..........((((.((.(((((((.......))).))))...))))))...................))).)))).))...... (-22.85 = -22.63 +  -0.22)

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 09:47:14 2006