Locus 5653

Sequence ID 3R_DroMel_CAF1
Location 14,836,177 – 14,836,607
Length 430
Max. P 0.908321
window9234 window9235 window9236 window9237 window9238 window9239 window9240

overview

Window 4

Location 14,836,177 – 14,836,296
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -38.35
Consensus MFE -35.52
Energy contribution -35.52
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.93
SVM decision value 1.06
SVM RNA-class probability 0.908321
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836177 119 + 27905053
AGCCACUAUCUCAAAGAUGGCCCAUUUGGGCGGCUCUCGCUGUCGUUGUUGUUGCCGUAUUUGC-CGUCUUGACGGCACUUAAAUUGCAUUAUUAUAUACGGCUCGACAUUUAUGUGCAA
((((..((((.....))))((((....))))))))...((......(((((..(((((((.(((-(((....))))))....(((......)))..))))))).))))).......)).. ( -39.32)
>DroSec_CAF1 14375 120 + 1
AGCCACUAUCUCAAAGAUGGCCCAUUUGGGCGGCUCUCGCUGUCGUUGUUGUUGCCGUAUUUGCCCGUCUUGACGGCACUUAAAUUGCAUUAUUAUAUACGGCUCGACAUUUAUGUGCAA
((((..((((.....))))((((....))))))))...((......(((((..(((((((.(((((((....))))..........))).......))))))).))))).......)).. ( -35.82)
>DroSim_CAF1 14517 120 + 1
AGCCACUAUCUCAAAGAUGGCCCAUUUGGGCGGCUCGCGCUGUCGUUGUUGUUGCCGUAUUUGCCCGUCUUGACGGCACUUAAAUUGCAUUAUUAUAUACGGCUCGACAUUUAUGUGCAA
((((..((((.....))))((((....)))))))).((((......(((((..(((((((.(((((((....))))..........))).......))))))).))))).....)))).. ( -39.90)
>consensus
AGCCACUAUCUCAAAGAUGGCCCAUUUGGGCGGCUCUCGCUGUCGUUGUUGUUGCCGUAUUUGCCCGUCUUGACGGCACUUAAAUUGCAUUAUUAUAUACGGCUCGACAUUUAUGUGCAA
((((..((((.....))))((((....))))))))...((......(((((..(((((((.(((.(((....))))))....(((......)))..))))))).))))).......)).. (-35.52 = -35.52 +  -0.00)

alignment

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secondary structure

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Window 5

Location 14,836,177 – 14,836,296
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -34.53
Consensus MFE -33.27
Energy contribution -33.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.96
SVM decision value 0.70
SVM RNA-class probability 0.826411
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836177 119 - 27905053
UUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACG-GCAAAUACGGCAACAACAACGACAGCGAGAGCCGCCCAAAUGGGCCAUCUUUGAGAUAGUGGCU
..((.(((...((((..(((((((....(((......)))..((((((....)))-))).))))))).....(((.((..((....)).((((....))))..)).))).))))))))). ( -36.90)
>DroSec_CAF1 14375 120 - 1
UUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACGGGCAAAUACGGCAACAACAACGACAGCGAGAGCCGCCCAAAUGGGCCAUCUUUGAGAUAGUGGCU
..((.(((...((((..(((((((....(((......)))..((((((....)).)))).))))))).....(((.((..((....)).((((....))))..)).))).))))))))). ( -33.10)
>DroSim_CAF1 14517 120 - 1
UUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACGGGCAAAUACGGCAACAACAACGACAGCGCGAGCCGCCCAAAUGGGCCAUCUUUGAGAUAGUGGCU
..((.(((...((((..(((((((....(((......)))..((((((....)).)))).))))))).....(((.((..((....)).((((....))))..)).))).))))))))). ( -33.60)
>consensus
UUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACGGGCAAAUACGGCAACAACAACGACAGCGAGAGCCGCCCAAAUGGGCCAUCUUUGAGAUAGUGGCU
..((.(((...((((..(((((((....(((......)))..((((((....))).))).))))))).....(((.((..((....)).((((....))))..)).))).))))))))). (-33.27 = -33.27 +   0.00)

alignment

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secondary structure

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Window 6

Location 14,836,217 – 14,836,336
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -25.42
Consensus MFE -24.15
Energy contribution -24.15
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.95
SVM decision value 0.20
SVM RNA-class probability 0.628995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836217 119 - 27905053
GAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACG-GCAAAUACGGCAACAACAACGACA
........((((((((....................)))))))).......(((((.(((((((....(((......)))..((((((....)))-))).)))))))........))))) ( -27.95)
>DroSec_CAF1 14415 120 - 1
GAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACGGGCAAAUACGGCAACAACAACGACA
........((((((((....................)))))))).......(((((.(((((((....(((......)))..((((((....)).)))).)))))))........))))) ( -24.15)
>DroSim_CAF1 14557 120 - 1
GAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACGGGCAAAUACGGCAACAACAACGACA
........((((((((....................)))))))).......(((((.(((((((....(((......)))..((((((....)).)))).)))))))........))))) ( -24.15)
>consensus
GAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUAAGUGCCGUCAAGACGGGCAAAUACGGCAACAACAACGACA
........((((((((....................)))))))).......(((((.(((((((....(((......)))..((((((....))).))).)))))))........))))) (-24.15 = -24.15 +   0.00)

alignment

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secondary structure

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Window 7

Location 14,836,256 – 14,836,376
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.32
Mean single sequence MFE -24.72
Consensus MFE -24.55
Energy contribution -24.55
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.99
SVM decision value 0.24
SVM RNA-class probability 0.649760
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836256 120 - 27905053
AGCCAAAUUCUUUUUUGCGGCUCUUUUUCCAUCAAUGGACGAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUA
.((...(((.((...(((((((((((.((((....)))).))).....((((((((....................))))))))...........))))))))...)).)))))...... ( -25.05)
>DroSec_CAF1 14455 117 - 1
--CCAAAUUCUU-UUUGCGGCUCUUUUUCCAUCAAUGGACGAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUA
--..........-..(((((((((((.((((....)))).))).....((((((((....................))))))))...........))))))))................. ( -24.55)
>DroSim_CAF1 14597 117 - 1
--CCAAAUUCUU-UUUGCGGCUCUUUUUCCAUCAAUGGACGAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUA
--..........-..(((((((((((.((((....)))).))).....((((((((....................))))))))...........))))))))................. ( -24.55)
>consensus
__CCAAAUUCUU_UUUGCGGCUCUUUUUCCAUCAAUGGACGAAGCGAAGCAAAUGUGUCCAACUUUGAACGAUAAAAUAUUUGCACAUAAAUGUCGAGCCGUAUAUAAUAAUGCAAUUUA
...............(((((((((((.((((....)))).))).....((((((((....................))))))))...........))))))))................. (-24.55 = -24.55 +   0.00)

alignment

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secondary structure

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Window 8

Location 14,836,336 – 14,836,456
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.96
Mean single sequence MFE -30.03
Consensus MFE -27.48
Energy contribution -27.26
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 0.91
SVM decision value 0.10
SVM RNA-class probability 0.582211
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836336 120 - 27905053
UUUAGGCCAUAAAGAAAUGCCUGAAUCCGACAAUGAGUCUGGGCUUUGGCUCUUUCUCCUUUCUUUUGAGAGCAGCAGCCAGCCAAAUUCUUUUUUGCGGCUCUUUUUCCAUCAAUGGAC
(((((((.((......))))))))).(((.(((.((((...((((..(((((((((((.........))))).)).))))))))..))))....)))))).......((((....)))). ( -32.40)
>DroSec_CAF1 14535 115 - 1
UUUAGGCCAUAACGAAAUGCCUGAAUCCGACAAUGAGUCUGGGCCUUGGCUCUUUCUCCUUUCUUUUGAGAGCAGCAG----CCAAAUUCUU-UUUGCGGCUCUUUUUCCAUCAAUGGAC
(((((((.((......)))))))))((((((.....))).((((((((((((((((((.........))))).)).))----))))......-.....))))).............))). ( -29.60)
>DroSim_CAF1 14677 111 - 1
CUUAGGCCAUA----AAUGCCUGAAUCCGACAAUGAGUCUGGGUCUUGGCUCUUUCUCCUUUCUUUUGAGAGCAGCAG----CCAAAUUCUU-UUUGCGGCUCUUUUUCCAUCAAUGGAC
.((((((....----...))))))..........(((((.(((..(((((((((((((.........))))).)).))----))))..))).-.....)))))....((((....)))). ( -28.10)
>consensus
UUUAGGCCAUAA_GAAAUGCCUGAAUCCGACAAUGAGUCUGGGCCUUGGCUCUUUCUCCUUUCUUUUGAGAGCAGCAG____CCAAAUUCUU_UUUGCGGCUCUUUUUCCAUCAAUGGAC
.((((((.((......)))))))).((((.....(((...((((....))))...))).........((((((.((((................)))).))))))..........)))). (-27.48 = -27.26 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,836,416 – 14,836,527
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -28.30
Consensus MFE -23.57
Energy contribution -25.57
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.83
SVM decision value 0.47
SVM RNA-class probability 0.750437
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836416 111 - 27905053
CCCACCCAC---------ACCAUGGAAAAUCUACAUAAAAACACACUUGAGCUAGAUUUCCAAUGGCCAAAGUGAGGCAGUUUAGGCCAUAAAGAAAUGCCUGAAUCCGACAAUGAGUCU
..(((....---------.(((((((((.(((((.(((........))).).))))))))).)))).....))).((..((((((((.((......))))))))))))(((.....))). ( -24.50)
>DroSec_CAF1 14610 120 - 1
CCCACCCACCAUGGAUUUUCCAUGGAAAAUCUACAUAAAAACACACUUGAGCUAGAUUUCCUAUGGCCAAAGUGAGGCAGUUUAGGCCAUAACGAAAUGCCUGAAUCCGACAAUGAGUCU
........((((((.....))))))..................(((((..((((.........))))..))))).((..((((((((.((......))))))))))))(((.....))). ( -31.00)
>DroSim_CAF1 14752 116 - 1
CCCACCCACCAUGGAUUUUCCAUGGAAAAUCUACAUAAAAACACACUUGAGCUAGAUUUCCAAUGGCCAAAGUGAGGCAGCUUAGGCCAUA----AAUGCCUGAAUCCGACAAUGAGUCU
............((((((..((((((((.(((((.(((........))).).))))))))).((((((.((((......)))).)))))).----.)))...))))))(((.....))). ( -29.40)
>consensus
CCCACCCACCAUGGAUUUUCCAUGGAAAAUCUACAUAAAAACACACUUGAGCUAGAUUUCCAAUGGCCAAAGUGAGGCAGUUUAGGCCAUAA_GAAAUGCCUGAAUCCGACAAUGAGUCU
........((((((.....))))))..................(((((..((((.........))))..))))).((..((((((((.((......))))))))))))(((.....))). (-23.57 = -25.57 +   2.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,836,496 – 14,836,607
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.53
Mean single sequence MFE -28.00
Consensus MFE -21.82
Energy contribution -24.27
Covariance contribution 2.45
Combinations/Pair 1.04
Mean z-score -2.87
Structure conservation index 0.78
SVM decision value 0.72
SVM RNA-class probability 0.833433
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14836496 111 - 27905053
UAACUGUGGAUGGAGGAGCUAGCUUACAUUGUGCCCCAACUCAGCAGUUUUUCAUCCCCCAAAAAAUUUCGAAAAUUACACCCACCCAC---------ACCAUGGAAAAUCUACAUAAAA
....(((((((.((((((((.(((....(((.....)))...)))))))))))................................(((.---------....)))...)))))))..... ( -18.10)
>DroSec_CAF1 14690 119 - 1
UAACUGUGGAUGGGGGAGC-AACUUACAUGGUGCCCCAACUCAGCAGUUUUUCAUCCCCCAAAAAAAUUCGUAAAUUACACCCACCCACCAUGGAUUUUCCAUGGAAAAUCUACAUAAAA
....(((((((((((((((-(.((.....)))))...((((....)))).....))))))............................((((((.....))))))...)))))))..... ( -32.10)
>DroSim_CAF1 14828 119 - 1
UAACUGUGGAGGGGGGAGC-AGCUUACAUGGUGCCCCAACUCAGCAGUUUUUCAUCCCCCAAAAAAUUUCGAAAAUUACACCCACCCACCAUGGAUUUUCCAUGGAAAAUCUACAUAAAA
.((((((.(((..(((.((-(.(......).))))))..))).)))))).......................................((((((.....))))))............... ( -33.80)
>consensus
UAACUGUGGAUGGGGGAGC_AGCUUACAUGGUGCCCCAACUCAGCAGUUUUUCAUCCCCCAAAAAAUUUCGAAAAUUACACCCACCCACCAUGGAUUUUCCAUGGAAAAUCUACAUAAAA
....(((((((((((((...((((.....(((......)))....)))).....))))))............................((((((.....))))))...)))))))..... (-21.82 = -24.27 +   2.45)

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 12:00:50 2006