Locus 6560

Sequence ID X_DroMel_CAF1
Location 16,411,071 – 16,411,223
Length 152
Max. P 0.859665
window10711 window10712

overview

Window 1

Location 16,411,071 – 16,411,189
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.95
Mean single sequence MFE -26.57
Consensus MFE -21.84
Energy contribution -21.77
Covariance contribution -0.06
Combinations/Pair 1.11
Mean z-score -1.56
Structure conservation index 0.82
SVM decision value 0.23
SVM RNA-class probability 0.642383
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16411071 118 + 22224390
CUACUCAAGCUAGUUAGCAGCAAAUGUAAGUAAGCGUCGUUCGUGUGACAUUUACCUUUCAGUUACACCGAUUAUCAAAAUA--CAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUAUCA
........(((....))).(((((((((.......((((...(((((((............)))))))))))........))--)))))))..(((((((......)))))))....... ( -28.26)
>DroSec_CAF1 31770 120 + 1
CUACCCAAGCUAGUUAGCAGCAAAUGUAAGUAAGCGUCGUUCGUGUGACAUUUACUUUUCAGUUACACCGAUUAUCAACAUACACAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUGUCA
........(((....))).((((((((..(....)((((...(((((((............)))))))))))...........))))))))..(((((((......)))))))....... ( -26.10)
>DroSim_CAF1 28000 120 + 1
CUACCCAAGCUAGUUAGCAGCAAAUGUAAGUAAGCGUCGUUCGUGUGACAUUUACUUUUUAGUUACACCGAUUAUCAACAUACACAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUGUCA
........(((....))).(((((((((((((((.((((......)))).)))))))..(((((.....))))).........))))))))..(((((((......)))))))....... ( -26.20)
>DroYak_CAF1 29830 118 + 1
CUACUCAAGCUAGUUAGCAGCAAAUGUCACUAGACGUCGUUCGUGUGACAGUUACUUUCCAGCAGUACCGAUUAUCAAGAUA--CAUUUGCAUUUUGCAUAGUUAAGUGCAAGUACGUCA
.((((...(((.(..((.(((...((((((...(((.....)))))))))))).))..).)))))))...........(((.--.((((((((((.((...)).))))))))))..))). ( -25.70)
>consensus
CUACCCAAGCUAGUUAGCAGCAAAUGUAAGUAAGCGUCGUUCGUGUGACAUUUACUUUUCAGUUACACCGAUUAUCAACAUA__CAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUGUCA
........(((....))).(((((((.........((((...(((((((............)))))))))))............)))))))..(((((((......)))))))....... (-21.84 = -21.77 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,411,111 – 16,411,223
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.57
Mean single sequence MFE -28.18
Consensus MFE -16.24
Energy contribution -16.43
Covariance contribution 0.19
Combinations/Pair 1.23
Mean z-score -2.74
Structure conservation index 0.58
SVM decision value 0.82
SVM RNA-class probability 0.859665
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16411111 112 + 22224390
UCGUGUGACAUUUACCUUUCAGUUACACCGAUUAUCAAAAUA--CAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUAUCAGA-----AAUGAACACACAACUGACCGU-GUCUACAUGAA
(((((((((((.......((((((..................--..(((((((((.((...)).)))))))))....(((..-----..)))......))))))..))-))).)))))). ( -25.80)
>DroSec_CAF1 31810 114 + 1
UCGUGUGACAUUUACUUUUCAGUUACACCGAUUAUCAACAUACACAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUGUCAGU-----AGUGAACACACAACUGACCGU-GUCUAUAUGAA
..(((((((............)))))))......(((....((((.(((((((((.((...)).)))))))))...((((((-----.(((....))).)))))).))-)).....))). ( -29.80)
>DroSim_CAF1 28040 114 + 1
UCGUGUGACAUUUACUUUUUAGUUACACCGAUUAUCAACAUACACAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUGUCAGU-----AGUGAACACACAACUGACCGU-GUCUAUAUGAA
..(((((((............)))))))......(((....((((.(((((((((.((...)).)))))))))...((((((-----.(((....))).)))))).))-)).....))). ( -29.80)
>DroYak_CAF1 29870 117 + 1
UCGUGUGACAGUUACUUUCCAGCAGUACCGAUUAUCAAGAUA--CAUUUGCAUUUUGCAUAGUUAAGUGCAAGUACGUCAGGACAUCAGUGGAC-UGCAGCUGUUCCUAAUCUACAAUGA
....(..((((((........(((((.(((....((..(((.--.((((((((((.((...)).))))))))))..)))..))......)))))-)))))))))..)............. ( -27.30)
>consensus
UCGUGUGACAUUUACUUUUCAGUUACACCGAUUAUCAACAUA__CAUUUGCAUUUUGCAUAGUUAAGUGCAAACAUGUCAGU_____AGUGAACACACAACUGACCGU_GUCUACAUGAA
(((((((((....((...((((((......................(((((((((.((...)).)))))))))...............(((....)))))))))..)).))).)))))). (-16.24 = -16.43 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:52 2006