Locus 1138

Sequence ID 3R_DroMel_CAF1
Location 3,400,139 – 3,400,403
Length 264
Max. P 0.757785
window1869 window1870 window1871

overview

Window 9

Location 3,400,139 – 3,400,243
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.29
Mean single sequence MFE -29.16
Consensus MFE -23.51
Energy contribution -24.32
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.41
Structure conservation index 0.81
SVM decision value 0.02
SVM RNA-class probability 0.543124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3400139 104 - 27905053
CAAAAUAGCCGGAAAAUUGGAAGCGAGCUGAAGGGCGCCGGCGGGCAAAUAUUGAAAAAUUCUUAUUUGAUUUUAAUGUUGUGCUUUU----------------UCCCACAUUUUCCGCA
.......((.((((((((((.((....))((((((((((....))).((((((((((...((......))))))))))))..))))))----------------).))).))))))))). ( -27.20)
>DroSim_CAF1 9090 104 - 1
CAAAAUAGCCGGAAAAUUGGAAGCGAGCUGAAGGGCGCCGGCGGGCAAAUAUUGAAAAAUUGUUAUUUGAUUUUAAUGUUGUGCUUUU----------------UCCCACAUUUUCCGCA
.......((.((((((((((.((....))((((((((((....))).((((((((((.............))))))))))..))))))----------------).))).))))))))). ( -25.92)
>DroEre_CAF1 7364 120 - 1
CAAAAUAGCCGGAAAAUUGGAAACGAGCUGAAGCGCGCCGGCGGGCAAAUAUUGAAAAAUUGUUAUUUGAUUUUAAUGUUGGGCUUUUGCCCGCAUUUCCGCAUUUCCGCAUUUUCCGCA
.......((.(((((((((((((...((....))(((...(((((((((..(..((((((((.....)))))))....)..)...))))))))).....))).)))))).))))))))). ( -38.90)
>DroYak_CAF1 12792 104 - 1
CAAAAUAGCCGGAAAAUUGGAAUCGAGCUGAAGGGCGCCGGCGGGCAAAUAUUGAAAAAUUGUUAUUUGAUUUUAAUGUUGUGCUUUU----------------UUCCACAUUUACCGCA
.......((.((.(((((((((..((((........(((....))).((((((((((.............))))))))))..))))..----------------))))).)))).)))). ( -24.62)
>consensus
CAAAAUAGCCGGAAAAUUGGAAGCGAGCUGAAGGGCGCCGGCGGGCAAAUAUUGAAAAAUUGUUAUUUGAUUUUAAUGUUGUGCUUUU________________UCCCACAUUUUCCGCA
.......((.((((((((((((....((((........))))(((((((((((((((.............)))))))))).)))))..................))))).))))))))). (-23.51 = -24.32 +   0.81)

alignment

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secondary structure

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Window 0

Location 3,400,163 – 3,400,283
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.06
Mean single sequence MFE -27.18
Consensus MFE -25.25
Energy contribution -25.25
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.93
SVM decision value 0.49
SVM RNA-class probability 0.757785
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3400163 120 + 27905053
AACAUUAAAAUCAAAUAAGAAUUUUUCAAUAUUUGCCCGCCGGCGCCCUUCAGCUCGCUUCCAAUUUUCCGGCUAUUUUGCCAUUGCUCUUCGCCAAUCGAGCUGUGUUCAAGUGCGCAA
...........((((((.((.....))..)))))).......((((.((((((((((.............(((......)))...((.....))....))))))).....))).)))).. ( -25.30)
>DroSim_CAF1 9114 120 + 1
AACAUUAAAAUCAAAUAACAAUUUUUCAAUAUUUGCCCGCCGGCGCCCUUCAGCUCGCUUCCAAUUUUCCGGCUAUUUUGCCAUUGCUCUUCGCCAAUCGAGCUGUGUUCAAGUGCGCAA
...........((((((............)))))).......((((.((((((((((.............(((......)))...((.....))....))))))).....))).)))).. ( -25.00)
>DroEre_CAF1 7404 120 + 1
AACAUUAAAAUCAAAUAACAAUUUUUCAAUAUUUGCCCGCCGGCGCGCUUCAGCUCGUUUCCAAUUUUCCGGCUAUUUUGCCAUUGCUCUUCGCCCAUCGAGCUGUGUUCAAGUGCGCAA
...........((((((............)))))).......(((((((((((((((.............(((......)))...((.....))....))))))).....)))))))).. ( -29.60)
>DroYak_CAF1 12816 120 + 1
AACAUUAAAAUCAAAUAACAAUUUUUCAAUAUUUGCCCGCCGGCGCCCUUCAGCUCGAUUCCAAUUUUCCGGCUAUUUUGCCAUUGCUCUUCGCCAAUCGAGCUGUGUUCAAGUGCGCAA
...........((((((............)))))).......((((.(((((((((((((..........(((......)))...((.....)).)))))))))).....))).)))).. ( -28.80)
>consensus
AACAUUAAAAUCAAAUAACAAUUUUUCAAUAUUUGCCCGCCGGCGCCCUUCAGCUCGCUUCCAAUUUUCCGGCUAUUUUGCCAUUGCUCUUCGCCAAUCGAGCUGUGUUCAAGUGCGCAA
...........((((((............)))))).......((((.((((((((((.............(((......)))...((.....))....))))))).....))).)))).. (-25.25 = -25.25 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,400,283 – 3,400,403
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.91
Mean single sequence MFE -33.35
Consensus MFE -32.97
Energy contribution -33.23
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.99
SVM decision value 0.29
SVM RNA-class probability 0.672159
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3400283 120 + 27905053
CUAACAAGCCACUUUGAGUGCUGCCACUUUGGUUGAUGUGGCUCGUAUUUACCUGUUUACCGAGUGGAGCCCUCAACGCUGGCCUAAGCCUAUUUCGGUUUAAGUUUUUUUUUUGCGCCC
..(((..(((((.(((((.(((.((((((.(((.((((.((..........)))))).)))))))))))).))))).).)))).((((((......)))))).))).............. ( -34.40)
>DroSim_CAF1 9234 117 + 1
CUAACAAGCCACUUUGAGUGCUGCCACUUUGGUUGAUGUGGCUCGUAUUUACCUGUUUACCGAGUGGAGCCCUCAACGCUGGCCUAAGCCUAUUUCGGUUUAAGUUUU---UUUGCGCCC
..(((..(((((.(((((.(((.((((((.(((.((((.((..........)))))).)))))))))))).))))).).)))).((((((......)))))).)))..---......... ( -34.40)
>DroEre_CAF1 7524 116 + 1
CUAACAAGCCACUUUGAGUGCUGCCACUUUAGUUGAUGUGGCUCGUAUUUACCUGUUUACCGAGUGGAGCCCUCAACGCUGGCCUAAGCCUAUUUCGGUUUAAGUUUU----UUGCACCC
..(((..(((((.(((((.(((.((((((..((.((((.((..........)))))).)).))))))))).))))).).)))).((((((......)))))).)))..----........ ( -30.20)
>DroYak_CAF1 12936 117 + 1
CUAACAAGCCACUUUGAGUGCUGCCACUUUGGUUGAUGUGGCUCGUAUUUACCUGUUUACCGAGUGGAGCCCUCAACGCUGGCCUAAGCCUAUUUCGGUUUAAGUUUU---UUUUCACCC
..(((..(((((.(((((.(((.((((((.(((.((((.((..........)))))).)))))))))))).))))).).)))).((((((......)))))).)))..---......... ( -34.40)
>consensus
CUAACAAGCCACUUUGAGUGCUGCCACUUUGGUUGAUGUGGCUCGUAUUUACCUGUUUACCGAGUGGAGCCCUCAACGCUGGCCUAAGCCUAUUUCGGUUUAAGUUUU___UUUGCACCC
..(((..(((((.(((((.(((.((((((.(((.((((.((..........)))))).)))))))))))).))))).).)))).((((((......)))))).))).............. (-32.97 = -33.23 +   0.25)

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 10:02:00 2006