Locus 4307

Sequence ID 3R_DroMel_CAF1
Location 11,424,369 – 11,424,510
Length 141
Max. P 0.999624
window7020 window7021 window7022

overview

Window 0

Location 11,424,369 – 11,424,470
Length 101
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.15
Mean single sequence MFE -25.92
Consensus MFE -22.18
Energy contribution -22.38
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.86
SVM decision value 2.37
SVM RNA-class probability 0.993082
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11424369 101 + 27905053
-------------AAGCACCCAUAUUCGCCCAGUUGGGCGCACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUAUAUAC------AUAUAUA
-------------((((((........((((....))))((.((....)))).......((((((...)))))).........)))))).........((((((...------.)))))) ( -23.50)
>DroSec_CAF1 171908 97 + 1
-------------AAGCACCCAUAUUCGCCCAGUUGGGCGCACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAAAGUGCUUGGCUAUCUUUGUAUAU----------AUAUA
-------------.(((.........(((((....))))).........((((((((..((((((...))))))......))))))))..)))............----------..... ( -23.20)
>DroSim_CAF1 166124 110 + 1
UGGCGGGAUCCCAAAGCACCCAUAUUCGCCCAUUUGGGCGCACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUGUAUAU----------AUAUA
((((((....)).((((((........((((....))))((.((....)))).......((((((...)))))).........)))))).))))...........----------..... ( -29.60)
>DroEre_CAF1 161613 93 + 1
-------------AAGCACCCAUAUUCGCCCAGUUGGGCGCACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUA--------------UAUA
-------------((((((........((((....))))((.((....)))).......((((((...)))))).........)))))).............--------------.... ( -23.00)
>DroYak_CAF1 164185 107 + 1
-------------AAGCCCGCAUAUUCGCCCAGUUGGGCGCACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUAUAUACUCGUAUAUAUAUA
-------------.((((.((((....((((....))))((.((....)))).......((((((...)))))).........))))..)))).....((((((((....)))))))).. ( -30.30)
>consensus
_____________AAGCACCCAUAUUCGCCCAGUUGGGCGCACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUAUAU__________AUAUA
.............((((((........((((....))))((.((....)))).......((((((...)))))).........))))))............................... (-22.18 = -22.38 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,424,369 – 11,424,470
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.15
Mean single sequence MFE -27.74
Consensus MFE -23.96
Energy contribution -24.36
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.28
Structure conservation index 0.86
SVM decision value 3.80
SVM RNA-class probability 0.999624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11424369 101 - 27905053
UAUAUAU------GUAUAUAUAAAGAUAGCCAAGCACUAUAGUAAUCGACUCAAUGAGUCAUAAAAAUGCCAAAAAUGUGCGCCCAACUGGGCGAAUAUGGGUGCUU-------------
((((((.------...)))))).........(((((((...(((.(((((((...)))))........((((....)).))((((....)))))).))).)))))))------------- ( -27.20)
>DroSec_CAF1 171908 97 - 1
UAUAU----------AUAUACAAAGAUAGCCAAGCACUUUAGUAAUCGACUCAAUGAGUCAUAAAAAUGCCAAAAAUGUGCGCCCAACUGGGCGAAUAUGGGUGCUU-------------
.....----------................((((((((........(((((...)))))...............((((.(((((....))))).))))))))))))------------- ( -25.20)
>DroSim_CAF1 166124 110 - 1
UAUAU----------AUAUACAAAGAUAGCCAAGCACUAUAGUAAUCGACUCAAUGAGUCAUAAAAAUGCCAAAAAUGUGCGCCCAAAUGGGCGAAUAUGGGUGCUUUGGGAUCCCGCCA
.....----------.........(((..(((((((((...(((.(((((((...)))))........((((....)).))((((....)))))).))).))))).)))).)))...... ( -30.80)
>DroEre_CAF1 161613 93 - 1
UAUA--------------UAUAAAGAUAGCCAAGCACUAUAGUAAUCGACUCAAUGAGUCAUAAAAAUGCCAAAAAUGUGCGCCCAACUGGGCGAAUAUGGGUGCUU-------------
....--------------.............(((((((...(((.(((((((...)))))........((((....)).))((((....)))))).))).)))))))------------- ( -26.10)
>DroYak_CAF1 164185 107 - 1
UAUAUAUAUACGAGUAUAUAUAAAGAUAGCCAAGCACUAUAGUAAUCGACUCAAUGAGUCAUAAAAAUGCCAAAAAUGUGCGCCCAACUGGGCGAAUAUGCGGGCUU-------------
(((((((((....))))))))).....((((..((............(((((...)))))...............((((.(((((....))))).)))))).)))).------------- ( -29.40)
>consensus
UAUAU__________AUAUAUAAAGAUAGCCAAGCACUAUAGUAAUCGACUCAAUGAGUCAUAAAAAUGCCAAAAAUGUGCGCCCAACUGGGCGAAUAUGGGUGCUU_____________
...............................(((((((...(((.(((((((...)))))........((((....)).))((((....)))))).))).)))))))............. (-23.96 = -24.36 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,424,396 – 11,424,510
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -28.60
Consensus MFE -24.02
Energy contribution -24.62
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -2.85
Structure conservation index 0.84
SVM decision value 3.21
SVM RNA-class probability 0.998745
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11424396 114 + 27905053
CACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUAUAUAC------AUAUAUAAAAACGAAAGAUAUAUUUGCGCUCGUAGUGAAAUGCUUGU
.........((((((....((((((...)))))).((((((((((((..(..(((((((.(((((..------..)))))......)))))))..)..))))).)))))))))))))... ( -27.50)
>DroSec_CAF1 171935 110 + 1
CACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAAAGUGCUUGGCUAUCUUUGUAUAU----------AUAUAAAUACGAAAGAUAUAUUUGCGCUCGUAGUGAACUGCUAGU
.......((((((......((((((...)))))).((((((.(((((..(..(((((((((((..----------......)))).)))))))..)..)))))..))))))..)))))). ( -29.30)
>DroSim_CAF1 166164 110 + 1
CACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUGUAUAU----------AUAUAAAUACGAAAGAUAUAUUUGCGCUCGUAGUGAACUGCUAGU
.......((((((......((((((...)))))).((((((((((((..(..(((((((((((..----------......)))).)))))))..)..))))).)))))))..)))))). ( -31.00)
>DroEre_CAF1 161640 106 + 1
CACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUA--------------UAUAUGUACGAAAGAUAUAUUUGUGCUCGUAGUGAACUGCCUGA
.........((((......((((((...)))))).(((((((((..(..(..(((((((.((--------------(....)))..)))))))..)..)..)).)))))))..))))... ( -25.80)
>DroYak_CAF1 164212 120 + 1
CACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUAUAUACUCGUAUAUAUAUAUGUACGAAAGAUAUAUUUUCGCUCGUAGUGAACUGCCUGA
.........((((......((((((...)))))).(((((((((((......((((((.........((((((((....))))))))))))))......)))).)))))))..))))... ( -29.40)
>consensus
CACAUUUUUGGCAUUUUUAUGACUCAUUGAGUCGAUUACUAUAGUGCUUGGCUAUCUUUAUAUAU__________AUAUAAAUACGAAAGAUAUAUUUGCGCUCGUAGUGAACUGCUUGU
.........((((......((((((...)))))).((((((((((((.....(((((((.((((((........))))))......))))))).....))))).)))))))..))))... (-24.02 = -24.62 +   0.60)

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 11:25:31 2006