Locus 4692

Sequence ID 2L_DroMel_CAF1
Location 13,485,088 – 13,485,270
Length 182
Max. P 0.999985
window7419 window7420 window7421 window7422 window7423

overview

Window 9

Location 13,485,088 – 13,485,204
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.87
Mean single sequence MFE -27.10
Consensus MFE -27.10
Energy contribution -27.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 1.00
SVM decision value 3.12
SVM RNA-class probability 0.998506
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13485088 116 + 22407834
---AAAAAAACAAC-ACCAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
---...........-.....(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). ( -27.10)
>DroVir_CAF1 134476 117 + 1
---ACAACAACAACAAACAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
---.................(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). ( -27.10)
>DroGri_CAF1 92985 117 + 1
---ACAACAACAACAAACAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
---.................(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). ( -27.10)
>DroEre_CAF1 88563 115 + 1
---AAA-AAACAAC-ACCAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
---...-.......-.....(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). ( -27.10)
>DroWil_CAF1 134224 115 + 1
---AAC-AAAAAAA-AACAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
---...-.......-.....(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). ( -27.10)
>DroMoj_CAF1 113362 120 + 1
AGAACAACAACAACAAACAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
....................(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). ( -27.10)
>consensus
___AAAAAAACAAC_AACAAGAUGCAGGCCGCAUUGAUGCUAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCA
....................(((((.....)))))..(((((...((((....)))).)))))...........((((((...((((((..(..........)..))))))..)))))). (-27.10 = -27.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,485,124 – 13,485,244
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 99.72
Mean single sequence MFE -35.28
Consensus MFE -35.15
Energy contribution -35.32
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.79
Structure conservation index 1.00
SVM decision value 4.96
SVM RNA-class probability 0.999965
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13485124 120 + 22407834
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGU
............(((((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))....))))))))). ( -35.90)
>DroEre_CAF1 88598 120 + 1
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGU
............(((((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))....))))))))). ( -35.90)
>DroWil_CAF1 134259 120 + 1
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCAGAGU
..((((....)))).((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))))))))........ ( -32.20)
>DroYak_CAF1 85887 120 + 1
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGU
............(((((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))....))))))))). ( -35.90)
>DroMoj_CAF1 113402 120 + 1
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGU
............(((((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))....))))))))). ( -35.90)
>DroAna_CAF1 147877 120 + 1
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGU
............(((((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))....))))))))). ( -35.90)
>consensus
UAAGAUCGAAAUCUCGGGUGGCGAGAAGAAGAAAGCUACGAAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGU
............(((((((((((((.........((((((...((((((..(..........)..))))))..)))))).......(((((......)))))))))....))))))))). (-35.15 = -35.32 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,485,124 – 13,485,244
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 99.72
Mean single sequence MFE -33.61
Consensus MFE -33.61
Energy contribution -33.61
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.39
Structure conservation index 1.00
SVM decision value 5.38
SVM RNA-class probability 0.999985
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13485124 120 - 22407834
ACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ ( -33.61)
>DroEre_CAF1 88598 120 - 1
ACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ ( -33.61)
>DroWil_CAF1 134259 120 - 1
ACUCUGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ ( -33.61)
>DroYak_CAF1 85887 120 - 1
ACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ ( -33.61)
>DroMoj_CAF1 113402 120 - 1
ACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ ( -33.61)
>DroAna_CAF1 147877 120 - 1
ACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ ( -33.61)
>consensus
ACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUUCGUAGCUUUCUUCUUCUCGCCACCCGAGAUUUCGAUCUUA
.(((.(((((....((((((((..(((((((..(((.(((((((.........))))))).))).................)))))))..)).))))))))))).)))............ (-33.61 = -33.61 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,485,164 – 13,485,270
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.88
Mean single sequence MFE -25.83
Consensus MFE -24.39
Energy contribution -24.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.94
SVM decision value 4.54
SVM RNA-class probability 0.999917
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13485164 106 + 22407834
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGUCAUGGGUAAUAAUAU--AA------AAUACCAAA------
....(((((((((.(((...((((((.((....))..))))))...(((((......)))))...))).)))))))))......((((.......--..------..))))...------ ( -26.40)
>DroSim_CAF1 85500 106 + 1
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGUCAUGGGUAAUAAUAU--AA------AAUACCAAA------
....(((((((((.(((...((((((.((....))..))))))...(((((......)))))...))).)))))))))......((((.......--..------..))))...------ ( -26.40)
>DroEre_CAF1 88638 106 + 1
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGUCAUGGGUAAUAAUAU--AA------AAUACCAAA------
....(((((((((.(((...((((((.((....))..))))))...(((((......)))))...))).)))))))))......((((.......--..------..))))...------ ( -26.40)
>DroWil_CAF1 134299 120 + 1
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCAGAGUCAUGGGUAAUAAUAAUUAACAAAUUAAAACCAAAAAAGAA
.......((((((.(((...((((((.((....))..))))))...(((((......)))))...))).)))))).......(((.((((............))))...)))........ ( -23.00)
>DroYak_CAF1 85927 106 + 1
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGUCAUGGGUAAUAAUAU--AA------AAUACCAAA------
....(((((((((.(((...((((((.((....))..))))))...(((((......)))))...))).)))))))))......((((.......--..------..))))...------ ( -26.40)
>DroAna_CAF1 147917 106 + 1
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGUCAUGGGUAAUAAUAU--AA------AAUACCAAA------
....(((((((((.(((...((((((.((....))..))))))...(((((......)))))...))).)))))))))......((((.......--..------..))))...------ ( -26.40)
>consensus
AAAAUUAGGUGGAAGACUUGAGUUGCCUAGUAAUGUAGCAACUAAAGAAAUAGCUCCAUUUCCUCGUUAUCCACCUGAGUCAUGGGUAAUAAUAU__AA______AAUACCAAA______
....(((((((((.(((...((((((...........))))))...(((((......)))))...))).)))))))))......((((...................))))......... (-24.39 = -24.73 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,485,164 – 13,485,270
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.88
Mean single sequence MFE -29.25
Consensus MFE -27.46
Energy contribution -27.79
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.47
Structure conservation index 0.94
SVM decision value 4.95
SVM RNA-class probability 0.999964
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13485164 106 - 22407834
------UUUGGUAUU------UU--AUAUUAUUACCCAUGACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
------...((((..------..--.......))))........(((((((..(((((((((((....)))))))))(((((((.........)))))))...))..)))))))...... ( -29.30)
>DroSim_CAF1 85500 106 - 1
------UUUGGUAUU------UU--AUAUUAUUACCCAUGACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
------...((((..------..--.......))))........(((((((..(((((((((((....)))))))))(((((((.........)))))))...))..)))))))...... ( -29.30)
>DroEre_CAF1 88638 106 - 1
------UUUGGUAUU------UU--AUAUUAUUACCCAUGACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
------...((((..------..--.......))))........(((((((..(((((((((((....)))))))))(((((((.........)))))))...))..)))))))...... ( -29.30)
>DroWil_CAF1 134299 120 - 1
UUCUUUUUUGGUUUUAAUUUGUUAAUUAUUAUUACCCAUGACUCUGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
.........(((..((((.........))))..))).........((((((..(((((((((((....)))))))))(((((((.........)))))))...))..))))))....... ( -29.00)
>DroYak_CAF1 85927 106 - 1
------UUUGGUAUU------UU--AUAUUAUUACCCAUGACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
------...((((..------..--.......))))........(((((((..(((((((((((....)))))))))(((((((.........)))))))...))..)))))))...... ( -29.30)
>DroAna_CAF1 147917 106 - 1
------UUUGGUAUU------UU--AUAUUAUUACCCAUGACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
------...((((..------..--.......))))........(((((((..(((((((((((....)))))))))(((((((.........)))))))...))..)))))))...... ( -29.30)
>consensus
______UUUGGUAUU______UU__AUAUUAUUACCCAUGACUCAGGUGGAUAACGAGGAAAUGGAGCUAUUUCUUUAGUUGCUACAUUACUAGGCAACUCAAGUCUUCCACCUAAUUUU
.........((((...................))))........(((((((..(((((((((((....)))))))))(((((((.........)))))))...))..)))))))...... (-27.46 = -27.79 +   0.33)

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 11:24:49 2006