Locus 2709

Sequence ID 2R_DroMel_CAF1
Location 9,517,682 – 9,517,838
Length 156
Max. P 0.999780
window4478 window4479 window4480 window4481

overview

Window 8

Location 9,517,682 – 9,517,801
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -24.55
Consensus MFE -23.39
Energy contribution -23.45
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.40
Structure conservation index 0.95
SVM decision value 1.77
SVM RNA-class probability 0.976654
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9517682 119 + 20766785
UACUAAGUAACUGAGGAAAAUGGAGAAAA-AAAAAUACUAGAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAG
..((..((((((.................-.......(((......)))........((((((((((.......(((.(((.....))).)))....))))))))))))))))..))... ( -23.90)
>DroSec_CAF1 14676 120 + 1
UACUAAGUAACUGAGGAAAAUAGAGAAAGAAGAAGUACUAGAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAG
..((..((((((.........................(((......)))........((((((((((.......(((.(((.....))).)))....))))))))))))))))..))... ( -23.90)
>DroSim_CAF1 14697 120 + 1
UACUAAGUAACUGAGGAAAAUAGAGAAAGAAAAAAUACUAGAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAG
..((..((((((.........................(((......)))........((((((((((.......(((.(((.....))).)))....))))))))))))))))..))... ( -23.90)
>DroYak_CAF1 14539 118 + 1
UACUAAGUAACCGAGGAAAAUAGAGAAAAGAAAAAUACUAGAAAAAUG--GGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAG
..((..((((((.........................(((......))--)......((((((((((.......(((.(((.....))).)))....))))))))))))))))..))... ( -26.50)
>consensus
UACUAAGUAACUGAGGAAAAUAGAGAAAAAAAAAAUACUAGAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAG
..((..((((((.........................(((......)))........((((((((((.......(((.(((.....))).)))....))))))))))))))))..))... (-23.39 = -23.45 +   0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,517,682 – 9,517,801
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -17.52
Consensus MFE -16.32
Energy contribution -16.32
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.93
SVM decision value 0.37
SVM RNA-class probability 0.708807
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9517682 119 - 20766785
CUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUCUAGUAUUUUU-UUUUCUCCAUUUUCCUCAGUUACUUAGUA
.....(((.....((((((((((.((..((((.............))))..))))))))))))........)))................-............................. ( -16.74)
>DroSec_CAF1 14676 120 - 1
CUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUCUAGUACUUCUUCUUUCUCUAUUUUCCUCAGUUACUUAGUA
.....(((.....((((((((((.((..((((.............))))..))))))))))))........))).............................................. ( -16.74)
>DroSim_CAF1 14697 120 - 1
CUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUCUAGUAUUUUUUCUUUCUCUAUUUUCCUCAGUUACUUAGUA
.....(((.....((((((((((.((..((((.............))))..))))))))))))........))).............................................. ( -16.74)
>DroYak_CAF1 14539 118 - 1
CUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCC--CAUUUUUCUAGUAUUUUUCUUUUCUCUAUUUUCCUCGGUUACUUAGUA
...((.((.((((((((((((((.((..((((.............))))..)))))))))))).......--........(((..............)))........)))).)).)).. ( -19.86)
>consensus
CUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUCUAGUAUUUUUUCUUUCUCUAUUUUCCUCAGUUACUUAGUA
......(....).((((((((((.((..((((.............))))..))))))))))))......................................................... (-16.32 = -16.32 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,517,721 – 9,517,838
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.72
Mean single sequence MFE -25.84
Consensus MFE -21.84
Energy contribution -21.84
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.85
SVM decision value 0.82
SVM RNA-class probability 0.859101
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9517721 117 + 20766785
GAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAGA---CAGAGAUGGAAAAUGCAGAGCGGGAGGGCGAUAUGA
.................((((((((((.......(((.(((.....))).)))....)))))))))).((((((.......---((....)).....(((...)))....)))))).... ( -24.50)
>DroSec_CAF1 14716 117 + 1
GAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAGA---CUGAGAUGGGAAGUGCAGAGCGGGAAGGCGAUAUGA
.......(((((((.....)))))))....((((((((((((.(((((....((((...(.....).)))).(((......---......)))...))))).)))..))))))))).... ( -28.30)
>DroSim_CAF1 14737 117 + 1
GAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAGA---CAGAGAUGGGAAGUGCAGAGCGGGAGGGCGAUAUGA
.......(((((((.....)))))))....((((((((((((.(((((....((((...(.....).)))).(((......---......)))...))))).)))..))))))))).... ( -27.90)
>DroEre_CAF1 14643 112 + 1
----GAUG-AUGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAGA---AAGAGAUGGGAAAUGCUGAGCGGGAGGGCGAUAUGA
----....-........((((((((((.......(((.(((.....))).)))....)))))))))).((((((.....(.---.((..((.....)).))...).....)))))).... ( -24.60)
>DroYak_CAF1 14579 118 + 1
GAAAAAUG--GGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAGAAAAAAGAGAUGGGAAAUGGUGAGCGGGAGGGCGAUAUGA
......((--(.((...((((((((((.......(((.(((.....))).)))....))))))))))..)).)))............................((......))....... ( -23.90)
>consensus
GAAAAAUGGGAGAGAAAUGUUUUCCCUGAAAUUGCUUUUGUUGUGUACACAAGACCAAGGGAAAACAGGUUGCCAAGAAGA___CAGAGAUGGGAAAUGCAGAGCGGGAGGGCGAUAUGA
.................((((((((((.......(((.(((.....))).)))....)))))))))).((((((....................................)))))).... (-21.84 = -21.84 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,517,721 – 9,517,838
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.72
Mean single sequence MFE -19.23
Consensus MFE -18.08
Energy contribution -18.08
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.94
SVM decision value 4.06
SVM RNA-class probability 0.999780
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9517721 117 - 20766785
UCAUAUCGCCCUCCCGCUCUGCAUUUUCCAUCUCUG---UCUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUC
.......((......)).................((---((.....))))...((((((((((.((..((((.............))))..))))))))))))................. ( -19.52)
>DroSec_CAF1 14716 117 - 1
UCAUAUCGCCUUCCCGCUCUGCACUUCCCAUCUCAG---UCUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUC
.......(((........(((............)))---.......)))....((((((((((.((..((((.............))))..))))))))))))................. ( -20.88)
>DroSim_CAF1 14737 117 - 1
UCAUAUCGCCCUCCCGCUCUGCACUUCCCAUCUCUG---UCUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUC
.......((......)).................((---((.....))))...((((((((((.((..((((.............))))..))))))))))))................. ( -19.52)
>DroEre_CAF1 14643 112 - 1
UCAUAUCGCCCUCCCGCUCAGCAUUUCCCAUCUCUU---UCUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCAU-CAUC----
.......(((..........................---.......)))....((((((((((.((..((((.............))))..))))))))))))........-....---- ( -17.93)
>DroYak_CAF1 14579 118 - 1
UCAUAUCGCCCUCCCGCUCACCAUUUCCCAUCUCUUUUUUCUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCC--CAUUUUUC
.......((......))............................(((.....((((((((((.((..((((.............))))..))))))))))))......)--))...... ( -18.32)
>consensus
UCAUAUCGCCCUCCCGCUCUGCAUUUCCCAUCUCUG___UCUUCUUGGCAACCUGUUUUCCCUUGGUCUUGUGUACACAACAAAAGCAAUUUCAGGGAAAACAUUUCUCUCCCAUUUUUC
.......(((....................................)))....((((((((((.((..((((.............))))..))))))))))))................. (-18.08 = -18.08 +   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 10:37:19 2006