Locus 1993

Sequence ID 3R_DroMel_CAF1
Location 5,640,254 – 5,640,445
Length 191
Max. P 0.994366
window3256 window3257 window3258 window3259 window3260

overview

Window 6

Location 5,640,254 – 5,640,374
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.81
Mean single sequence MFE -33.40
Consensus MFE -28.59
Energy contribution -28.78
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -2.27
Structure conservation index 0.86
SVM decision value 1.42
SVM RNA-class probability 0.951861
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5640254 120 - 27905053
CAAAAUGAUGGAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUUUUGCGGAGCACAAAGAAAAUGGUUUCCACAAGGUCUACGAAUUUGUUCACCAGGUACAAAGUGCAAAUCAAACGCU
.....((((((.((((..((((((((((((......))))))))))))((((..((.......))..)))).....))))..(((....))).))..((((...))))..))))...... ( -30.00)
>DroSec_CAF1 14081 120 - 1
CAAAAUGAUGGAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUCUUGCGGAGCACGAAGAAUAUCGUUUCCACAAGGUCCACGAAUUUGUUCAGCAUGUACAAAAUGCAAAUCAAACGCU
.....(((((((....((((((((((((((......))))))))))))((((.((((......))))))))))....))).............((((.......))))..))))...... ( -35.70)
>DroSim_CAF1 14785 120 - 1
CAAAAUGGUGAAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUCUUGCGGAGCACGAAGAAAAUCGUUUCCACAAGGUCUACGAAUUUGUUCAGCAUGUACAAAAUGCAAAUCAAACGCU
......((((..((((..((((((((((((......))))))))))))((((.((((......)))))))).....)))).....((((....((((.......))))....)))))))) ( -37.70)
>DroYak_CAF1 14983 120 - 1
AAAAGUGAUGAAAGACGUGCAGGAAGGAUAUCUGUUUGUCCUUCUUGCGGAGCACAAAGAAAACCGUUUCCACAAGGUCCACGAAUUUGUUAAACAUAUACAAAAUGCAUAUCGAACGCU
...((((........(((((((((((((((......))))))))))))(((.(.....((((....)))).....).))))))..(((((.........)))))............)))) ( -30.20)
>consensus
CAAAAUGAUGAAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUCUUGCGGAGCACAAAGAAAAUCGUUUCCACAAGGUCCACGAAUUUGUUCAGCAUGUACAAAAUGCAAAUCAAACGCU
.....((((....(((..((((((((((((......))))))))))))((((.((((......)))))))).....)))......(((((.........)))))......))))...... (-28.59 = -28.78 +   0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,640,294 – 5,640,414
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.67
Mean single sequence MFE -35.84
Consensus MFE -32.68
Energy contribution -32.86
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -2.81
Structure conservation index 0.91
SVM decision value 2.47
SVM RNA-class probability 0.994366
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5640294 120 + 27905053
AGACCUUGUGGAAACCAUUUUCUUUGUGCUCCGCAAAAAGGACAGACAGAUAUCCUUCCUGCACGUCUUCCAUCAUUUUGCGAUGGCAUUUUUUGGAUAUCUCUACUACUGCUUCCACGG
......(((((((......((((((.(((...))).))))))(((..((((((((....(((.((((...((......)).)))))))......))))))))......))).))))))). ( -29.20)
>DroSec_CAF1 14121 120 + 1
GGACCUUGUGGAAACGAUAUUCUUCGUGCUCCGCAAGAAGGACAGACAGAUAUCCUUCCUGCACGUCUUCCAUCAUUUUGCGAUGGCAUUUCUGGGAUAUCUGUACUACUACUUCCACGG
(((.((((((((.((((......))))..))))))))......(((((((((((((...(((.((((...((......)).))))))).....))))))))))).))......))).... ( -42.30)
>DroSim_CAF1 14825 120 + 1
AGACCUUGUGGAAACGAUUUUCUUCGUGCUCCGCAAGAAGGACAGACAGAUAUCCUUCCUGCACGUCUUUCACCAUUUUGCGAUGGCAUUUCUGGGAUAUCUCUACUACUACUUCCACGG
...(((((((((.((((......))))..)))))))((((...((..(((((((((...(((.((((..............))))))).....)))))))))...))....))))...)) ( -34.04)
>DroYak_CAF1 15023 120 + 1
GGACCUUGUGGAAACGGUUUUCUUUGUGCUCCGCAAGAAGGACAAACAGAUAUCCUUCCUGCACGUCUUUCAUCACUUUUCGAUGGCAUUUUUCGGAUAUCUGUAUUACUUUUUCCACGG
......((((((((.(((.....((((.((.(....).)).))))((((((((((....(((.((((..............)))))))......))))))))))...))).)))))))). ( -37.84)
>consensus
AGACCUUGUGGAAACGAUUUUCUUCGUGCUCCGCAAGAAGGACAGACAGAUAUCCUUCCUGCACGUCUUCCAUCAUUUUGCGAUGGCAUUUCUGGGAUAUCUCUACUACUACUUCCACGG
......(((((((......((((((.(((...))).)))))).(((((((((((((...(((.((((..............))))))).....))))))))))).)).....))))))). (-32.68 = -32.86 +   0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,640,294 – 5,640,414
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -37.69
Consensus MFE -34.62
Energy contribution -34.38
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -2.69
Structure conservation index 0.92
SVM decision value 2.43
SVM RNA-class probability 0.993825
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5640294 120 - 27905053
CCGUGGAAGCAGUAGUAGAGAUAUCCAAAAAAUGCCAUCGCAAAAUGAUGGAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUUUUGCGGAGCACAAAGAAAAUGGUUUCCACAAGGUCU
..((((((((.............(((........((((((.....)))))).......((((((((((((......)))))))))))))))..............))))))))....... ( -38.23)
>DroSec_CAF1 14121 120 - 1
CCGUGGAAGUAGUAGUACAGAUAUCCCAGAAAUGCCAUCGCAAAAUGAUGGAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUCUUGCGGAGCACGAAGAAUAUCGUUUCCACAAGGUCC
..(((((((..(((.........(((........((((((.....)))))).......((((((((((((......)))))))))))))))..........)))..)))))))....... ( -40.01)
>DroSim_CAF1 14825 120 - 1
CCGUGGAAGUAGUAGUAGAGAUAUCCCAGAAAUGCCAUCGCAAAAUGGUGAAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUCUUGCGGAGCACGAAGAAAAUCGUUUCCACAAGGUCU
..((((((...........(...(((.......(((((......))))).........((((((((((((......))))))))))))))).)((((......))))))))))....... ( -36.00)
>DroYak_CAF1 15023 120 - 1
CCGUGGAAAAAGUAAUACAGAUAUCCGAAAAAUGCCAUCGAAAAGUGAUGAAAGACGUGCAGGAAGGAUAUCUGUUUGUCCUUCUUGCGGAGCACAAAGAAAACCGUUUCCACAAGGUCC
..(((((((..((..........(((.........(((((.....)))))........((((((((((((......)))))))))))))))...........))..)))))))....... ( -36.50)
>consensus
CCGUGGAAGUAGUAGUACAGAUAUCCCAAAAAUGCCAUCGCAAAAUGAUGAAAGACGUGCAGGAAGGAUAUCUGUCUGUCCUUCUUGCGGAGCACAAAGAAAAUCGUUUCCACAAGGUCC
..(((((((..((..........(((........((((((.....)))))).......((((((((((((......)))))))))))))))...........))..)))))))....... (-34.62 = -34.38 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,640,334 – 5,640,445
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.60
Mean single sequence MFE -29.77
Consensus MFE -26.24
Energy contribution -26.87
Covariance contribution 0.63
Combinations/Pair 1.03
Mean z-score -1.63
Structure conservation index 0.88
SVM decision value 0.60
SVM RNA-class probability 0.794415
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5640334 111 + 27905053
GACAGACAGAUAUCCUUCCUGCACGUCUUCCAUCAUUUUGCGAUGGCAUUUUUUGGAUAUCUCUACUACUGCUUCCACGGAUACGGUGGCGUUGCCUUUCCACAGUGCCUG---------
.......((((((((....(((.((((...((......)).)))))))......)))))))).....((((..((....))..))))(((((((........)))))))..--------- ( -26.60)
>DroSec_CAF1 14161 111 + 1
GACAGACAGAUAUCCUUCCUGCACGUCUUCCAUCAUUUUGCGAUGGCAUUUCUGGGAUAUCUGUACUACUACUUCCACGGCUACGGUGGUGUUGCCUUUCCACAGUGCCUG---------
...(((((((((((((...(((.((((...((......)).))))))).....))))))))))).))...........(((.((.((((..........)))).)))))..--------- ( -33.50)
>DroSim_CAF1 14865 120 + 1
GACAGACAGAUAUCCUUCCUGCACGUCUUUCACCAUUUUGCGAUGGCAUUUCUGGGAUAUCUCUACUACUACUUCCACGGCUACGGUGGUGUUGCCUUUCCACAGUGCCUGCUAAACNNN
.......(((((((((...(((.((((..............))))))).....)))))))))................(((.((.((((..........)))).)))))........... ( -27.34)
>DroYak_CAF1 15063 111 + 1
GACAAACAGAUAUCCUUCCUGCACGUCUUUCAUCACUUUUCGAUGGCAUUUUUCGGAUAUCUGUAUUACUUUUUCCACGGAUACGGUGGAGUUGCAUUUCCACAGUGCCUG---------
.....((((((((((....(((.((((..............)))))))......))))))))))..............((.(((.((((((......)))))).)))))..--------- ( -31.64)
>consensus
GACAGACAGAUAUCCUUCCUGCACGUCUUCCAUCAUUUUGCGAUGGCAUUUCUGGGAUAUCUCUACUACUACUUCCACGGAUACGGUGGUGUUGCCUUUCCACAGUGCCUG_________
...(((((((((((((...(((.((((..............))))))).....))))))))))).))...........((.(((.((((..........)))).)))))........... (-26.24 = -26.87 +   0.63)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,640,334 – 5,640,445
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.60
Mean single sequence MFE -31.23
Consensus MFE -25.17
Energy contribution -25.05
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.39
Structure conservation index 0.81
SVM decision value -0.01
SVM RNA-class probability 0.530715
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5640334 111 - 27905053
---------CAGGCACUGUGGAAAGGCAACGCCACCGUAUCCGUGGAAGCAGUAGUAGAGAUAUCCAAAAAAUGCCAUCGCAAAAUGAUGGAAGACGUGCAGGAAGGAUAUCUGUCUGUC
---------((((((((((.....(....).((((.......))))..))))).....((((((((........((((((.....))))))....(.....)...))))))))))))).. ( -32.40)
>DroSec_CAF1 14161 111 - 1
---------CAGGCACUGUGGAAAGGCAACACCACCGUAGCCGUGGAAGUAGUAGUACAGAUAUCCCAGAAAUGCCAUCGCAAAAUGAUGGAAGACGUGCAGGAAGGAUAUCUGUCUGUC
---------..(((((.((((...(....).)))).)).)))..........(((.((((((((((((....))((((((.....))))))..............))))))))))))).. ( -35.70)
>DroSim_CAF1 14865 120 - 1
NNNGUUUAGCAGGCACUGUGGAAAGGCAACACCACCGUAGCCGUGGAAGUAGUAGUAGAGAUAUCCCAGAAAUGCCAUCGCAAAAUGGUGAAAGACGUGCAGGAAGGAUAUCUGUCUGUC
........((((((.(..(((...((........))....)))..)............((((((((......((((.((.((......))...)).).)))....)))))))))))))). ( -29.40)
>DroYak_CAF1 15063 111 - 1
---------CAGGCACUGUGGAAAUGCAACUCCACCGUAUCCGUGGAAAAAGUAAUACAGAUAUCCGAAAAAUGCCAUCGAAAAGUGAUGAAAGACGUGCAGGAAGGAUAUCUGUUUGUC
---------..(((((..((((.(((.........))).))))..)..........((((((((((......((((.((....(....)....)).).)))....)))))))))).)))) ( -27.40)
>consensus
_________CAGGCACUGUGGAAAGGCAACACCACCGUAGCCGUGGAAGUAGUAGUACAGAUAUCCCAAAAAUGCCAUCGCAAAAUGAUGAAAGACGUGCAGGAAGGAUAUCUGUCUGUC
.........(((((.(..(((...((........))....)))..)............((((((((......((((((((.....)))))........)))....))))))))))))).. (-25.17 = -25.05 +  -0.12)

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 10:24:36 2006