Locus 55

Sequence ID 4_DroMel_CAF1
Location 502,042 – 502,311
Length 269
Max. P 0.980909
window82 window83 window84 window85

overview

Window 2

Location 502,042 – 502,153
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 70.46
Mean single sequence MFE -25.63
Consensus MFE -14.64
Energy contribution -16.63
Covariance contribution 2.00
Combinations/Pair 1.12
Mean z-score -1.50
Structure conservation index 0.57
SVM decision value 0.08
SVM RNA-class probability 0.574366
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 502042 111 - 1281640
UCUUUUCCUUCCCUAGUGCGU-AUAGAGCGCUCAAAAUGAUCUAUAUUUUUCGUAUUAUAGACAACUGAUGUUUUG--------GCAUUUACUAUGCGUUCCGUAAGUCGCUCUGAAGAU
.......((((...(((((.(-(..((((((......((.((((((..........))))))))...(((((....--------)))))......))))))..)).).))))..)))).. ( -23.70)
>DroSec_CAF1 8324 102 - 1
-----------------GCGUUUUAGAGCGCCCAAAAUGAUCUGUAUAUUCCGU-UUAUAGUCAACUGAUGAUUUGGGCUAUAGGCAUUUACUAUGCGUUCCGUAAGUCGCUCUAAAGAU
-----------------...((((((((((((((((.(((.(((((........-.)))))))).(....).))))))).....((((.....))))............))))))))).. ( -28.50)
>DroSim_CAF1 8479 102 - 1
-----------------GCGUUUUAGAGCGCCCAAAAUGAUCUGUAUAUUCCGU-UUAUAGUCAACUGAUGAUUUGGGCUAUAGGCAUUUACUAUGCGUUCCGUAAGUCGUUCUAAAGAU
-----------------...((((((((((((((((.(((.(((((........-.)))))))).(....).))))))).....((((.....))))............))))))))).. ( -26.10)
>DroYak_CAF1 12864 101 - 1
UUUAUUCCCUCCCUGGUGCGUUAUAGAGCGCCCUAAAUGAUCUAUAU---------CAUAUUUAACUGAUGUUUUGGG----------UUAAUAUGGUGCCCGUAAGUUGCUCUAAGGAU
.........(((.(((.((((((..(.(((((.....((((((((((---------((........))))))...)))----------)))....))))))..)))..))).))).))). ( -24.20)
>consensus
_________________GCGUUAUAGAGCGCCCAAAAUGAUCUAUAUAUUCCGU_UUAUAGUCAACUGAUGAUUUGGG______GCAUUUACUAUGCGUUCCGUAAGUCGCUCUAAAGAU
....................((((((((((((((((((.(((.........................)))))))))))).............((((.....))))....))))))))).. (-14.64 = -16.63 +   2.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 502,153 – 502,272
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.94
Mean single sequence MFE -20.40
Consensus MFE -9.84
Energy contribution -10.28
Covariance contribution 0.44
Combinations/Pair 1.15
Mean z-score -2.32
Structure conservation index 0.48
SVM decision value 1.65
SVM RNA-class probability 0.969718
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 502153 119 + 1281640
UAACAUAAUUUGAAAAAAAAAAUAUUUCAACAGGCACAGCUUAAUAAAGAGCUGGAGAAAUAUCGAUGAAAACAUCGAUG-CAUGAUUUUUCAUAAAAAUCGAUAUUCAACAUUAUUCUU
....((((((((((...................((.((((((......)))))).......(((((((....))))))))-).(((((((.....)))))))...))))).))))).... ( -24.10)
>DroSec_CAF1 8426 104 + 1
---------------AAAAAAAUAUUUUAACAGGCACAGUUUAAGAAAGAGCUAGAAAAACAUCGAUGAAAACAUCGAUG-CAUGAUUUUUCAUAAAAAUCGAUAUUCAAAAUUAUUCUU
---------------......................(((((......))))).(((...((((((((....))))))))-..(((((((.....)))))))...)))............ ( -16.20)
>DroSim_CAF1 8581 104 + 1
---------------AAAAAAAUAUUUUAACAGGCACAGUUUAAGAAAGAGCUCGAAAAACAUCGAUGAAAACAUCGAUG-UAUGAUUUUUCAUAAAAAUCGAUAUUCAAAAUUAUUCUU
---------------......................((..(((....(((.((((...(((((((((....))))))))-)((((....)))).....))))..)))....)))..)). ( -17.80)
>DroYak_CAF1 12965 96 + 1
UAACAUUAGUUGAAGAC--GAUGAUUUCAACAGGCACGGCUUAGG----------------AUCGAUAAUAACAUCGAUUCCCUGAUGUUUUGUAAGAAUCGAUGUUCAAC------CCU
........((((((.((--(((..((.(((..(((((((....((----------------((((((......)))))))).))).))))))).))..)))).).))))))------... ( -23.50)
>consensus
_______________AAAAAAAUAUUUCAACAGGCACAGCUUAAGAAAGAGCU_GAAAAACAUCGAUGAAAACAUCGAUG_CAUGAUUUUUCAUAAAAAUCGAUAUUCAAAAUUAUUCUU
..........................................(((((.............((((((((....))))))))...(((((((.....))))))).............))))) ( -9.84 = -10.28 +   0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 502,153 – 502,272
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.94
Mean single sequence MFE -22.02
Consensus MFE -11.56
Energy contribution -13.12
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -2.19
Structure conservation index 0.52
SVM decision value 1.87
SVM RNA-class probability 0.980909
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 502153 119 - 1281640
AAGAAUAAUGUUGAAUAUCGAUUUUUAUGAAAAAUCAUG-CAUCGAUGUUUUCAUCGAUAUUUCUCCAGCUCUUUAUUAAGCUGUGCCUGUUGAAAUAUUUUUUUUUUCAAAUUAUGUUA
..((..((((((((((((((((...(((((....)))))-.)))))))).....))))))))..))(((((........)))))......((((((.........))))))......... ( -22.70)
>DroSec_CAF1 8426 104 - 1
AAGAAUAAUUUUGAAUAUCGAUUUUUAUGAAAAAUCAUG-CAUCGAUGUUUUCAUCGAUGUUUUUCUAGCUCUUUCUUAAACUGUGCCUGUUAAAAUAUUUUUUU---------------
(((((((.((((((.....((((((.....))))))..(-((((((((....))))))))).............................)))))))))))))..--------------- ( -18.60)
>DroSim_CAF1 8581 104 - 1
AAGAAUAAUUUUGAAUAUCGAUUUUUAUGAAAAAUCAUA-CAUCGAUGUUUUCAUCGAUGUUUUUCGAGCUCUUUCUUAAACUGUGCCUGUUAAAAUAUUUUUUU---------------
(((((..(.((((((....((((((.....))))))..(-((((((((....)))))))))..)))))).)..)))))...........................--------------- ( -20.30)
>DroYak_CAF1 12965 96 - 1
AGG------GUUGAACAUCGAUUCUUACAAAACAUCAGGGAAUCGAUGUUAUUAUCGAU----------------CCUAAGCCGUGCCUGUUGAAAUCAUC--GUCUUCAACUAAUGUUA
(((------(((((((((((((((((...........)))))))))))).....)))))----------------)))....(((....((((((......--...))))))..)))... ( -26.50)
>consensus
AAGAAUAAUGUUGAAUAUCGAUUUUUAUGAAAAAUCAUG_CAUCGAUGUUUUCAUCGAUGUUUUUC_AGCUCUUUCUUAAACUGUGCCUGUUAAAAUAUUUUUUU_______________
..(((.((((((((((((((((...(((((....)))))..)))))))).....)))))))).)))...................................................... (-11.56 = -13.12 +   1.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 502,193 – 502,311
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 93.50
Mean single sequence MFE -23.73
Consensus MFE -18.57
Energy contribution -18.47
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.78
SVM decision value 0.01
SVM RNA-class probability 0.540848
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 502193 118 + 1281640
UUAAUAAAGAGCUGGAGAAAUAUCGAUGAAAACAUCGAUGCAUGAUUUUUCAUAAAAAUCGAUAUUCAACAUUAUUCUUCUUUGCGCCCAUAUAUGUAGGAUAACGAAAUCUCUACAC
..........((.((((((.((((((((....))))))))..(((((((.....))))))).............))))))...)).........((((((((......))).))))). ( -25.50)
>DroSec_CAF1 8451 118 + 1
UUAAGAAAGAGCUAGAAAAACAUCGAUGAAAACAUCGAUGCAUGAUUUUUCAUAAAAAUCGAUAUUCAAAAUUAUUCUUCUUUGUGCCCAUUAAUGUCGGAUAACGAAAUUUCUACAC
...((((((.((.((((...((((((((....))))))))..(((((((.....)))))))................))))....)).).......(((.....)))..))))).... ( -21.40)
>DroSim_CAF1 8606 118 + 1
UUAAGAAAGAGCUCGAAAAACAUCGAUGAAAACAUCGAUGUAUGAUUUUUCAUAAAAAUCGAUAUUCAAAAUUAUUCUUCUUUGUGCCCAUUAAUGUCGGAUAACGAAAUUUCUACAC
...((((((.((.((((..(((((((((....))))))))).(((((((.....)))))))...................)))).)).).......(((.....)))..))))).... ( -24.30)
>consensus
UUAAGAAAGAGCUAGAAAAACAUCGAUGAAAACAUCGAUGCAUGAUUUUUCAUAAAAAUCGAUAUUCAAAAUUAUUCUUCUUUGUGCCCAUUAAUGUCGGAUAACGAAAUUUCUACAC
..........(.((((((..((((((((....))))))))..(((((((.....)))))))...................(((((.((.((....)).))...))))).))))))).. (-18.57 = -18.47 +  -0.11)

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 09:32:46 2006