Locus 1390

Sequence ID X_DroMel_CAF1
Location 4,175,751 – 4,175,885
Length 134
Max. P 0.969065
window2215 window2216 window2217

overview

Window 5

Location 4,175,751 – 4,175,849
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 92.86
Mean single sequence MFE -25.28
Consensus MFE -17.94
Energy contribution -18.62
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -2.36
Structure conservation index 0.71
SVM decision value 0.05
SVM RNA-class probability 0.558261
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4175751 98 + 22224390
AGGCUCGUAUCUGUAUCUGGGCAUCGAUAAAUGCCCAAGUGCAUAGAGUAAUUACUACUUUUCGCCAUAUUUAUUCGAGAGGUACAAGUACUACUUGA
.(((.......((((..(((((((......)))))))..)))).((((((.....))))))..)))........(((((.((((....)))).))))) ( -30.70)
>DroSec_CAF1 8464 98 + 1
AAGCUCGUAUCUAUAUCUGGGCAUCGAUAAAUGCCCAAGUGCAUAGCGUAAUUACUACUUCUCGCCGUAUUUAUACGAGAGGUACAAGUACUACUUGA
..(((.(((.((.....(((((((......))))))))))))..)))........(((((((((...........)))))))))((((.....)))). ( -26.60)
>DroSim_CAF1 8864 98 + 1
AAGCUCGUAUAUAUAUCUGGGCAUCGAUAAAUGCCCAAGUGCAUAGCGUAAUUACUACUUCUCGCCGUAUUUAUACGAGAGGUACAAGUACUACUUGA
.....(((.(((.((..(((((((......)))))))..)).)))))).......(((((((((...........)))))))))((((.....)))). ( -27.10)
>DroEre_CAF1 8451 98 + 1
AAGCUCGUAUCUAUAACUAGGCAUCGAUAAAUGCCCAAGUGCAUAUCGUAAUUACUACUUCUCACCGUAUUUACUCGAUAGGCACAAGUACUGCUUGA
((((..((((.........(((((......)))))...((((.((((((((.(((...........))).))))..)))).))))..)))).)))).. ( -22.80)
>DroYak_CAF1 9347 98 + 1
AGGCUCGUAUCUAUAUCUAGGCAUCGAUAAAUGCCCAAGUGCAUAUCGUAAUUACUACUUCUCACCGUAUUUAUUCGAGAGGUACAAGUACUACUUGA
.(((...((((.((........)).))))...)))((((((......(((.....((((((((.............))))))))....))))))))). ( -19.22)
>consensus
AAGCUCGUAUCUAUAUCUGGGCAUCGAUAAAUGCCCAAGUGCAUAGCGUAAUUACUACUUCUCGCCGUAUUUAUUCGAGAGGUACAAGUACUACUUGA
.................(((((((......)))))))(((((.....((....))((((((((.............))))))))...)))))...... (-17.94 = -18.62 +   0.68)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,175,751 – 4,175,849
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 92.86
Mean single sequence MFE -24.52
Consensus MFE -19.14
Energy contribution -19.10
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -1.55
Structure conservation index 0.78
SVM decision value 0.10
SVM RNA-class probability 0.583679
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4175751 98 - 22224390
UCAAGUAGUACUUGUACCUCUCGAAUAAAUAUGGCGAAAAGUAGUAAUUACUCUAUGCACUUGGGCAUUUAUCGAUGCCCAGAUACAGAUACGAGCCU
((.((..(((....)))..)).))........(((.....((((........))))....(((((((((....)))))))))............))). ( -21.80)
>DroSec_CAF1 8464 98 - 1
UCAAGUAGUACUUGUACCUCUCGUAUAAAUACGGCGAGAAGUAGUAAUUACGCUAUGCACUUGGGCAUUUAUCGAUGCCCAGAUAUAGAUACGAGCUU
....((((((.((((((.((((((.........)))))).))).))).))).(((((...(((((((((....))))))))).))))).)))...... ( -27.40)
>DroSim_CAF1 8864 98 - 1
UCAAGUAGUACUUGUACCUCUCGUAUAAAUACGGCGAGAAGUAGUAAUUACGCUAUGCACUUGGGCAUUUAUCGAUGCCCAGAUAUAUAUACGAGCUU
.((((.....)))).....((((((((.(((.((((.((........)).))))......(((((((((....))))))))).))).))))))))... ( -27.20)
>DroEre_CAF1 8451 98 - 1
UCAAGCAGUACUUGUGCCUAUCGAGUAAAUACGGUGAGAAGUAGUAAUUACGAUAUGCACUUGGGCAUUUAUCGAUGCCUAGUUAUAGAUACGAGCUU
..((((.(((((.((((.((((((((...(((........)))...))).))))).))))(((((((((....)))))))))....)).)))..)))) ( -27.40)
>DroYak_CAF1 9347 98 - 1
UCAAGUAGUACUUGUACCUCUCGAAUAAAUACGGUGAGAAGUAGUAAUUACGAUAUGCACUUGGGCAUUUAUCGAUGCCUAGAUAUAGAUACGAGCCU
....((((((.((((((.(((((...........))))).))).))).))).........(((((((((....))))))))).......)))...... ( -18.80)
>consensus
UCAAGUAGUACUUGUACCUCUCGAAUAAAUACGGCGAGAAGUAGUAAUUACGCUAUGCACUUGGGCAUUUAUCGAUGCCCAGAUAUAGAUACGAGCUU
....((((((.((((((.(((((...........))))).))).))).))).........(((((((((....))))))))).......)))...... (-19.14 = -19.10 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,175,778 – 4,175,885
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 94.77
Mean single sequence MFE -28.02
Consensus MFE -23.92
Energy contribution -24.40
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.85
SVM decision value 1.64
SVM RNA-class probability 0.969065
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4175778 107 + 22224390
UAAAUGCCCAAGUGCAUAGAGUAAUUACUACUUUUCGCCAUAUUUAUUCGAGAGGUACAAGUACUACUUGAAGCGAAAGUAUCUCAAGGUAUUCCGGCAGCCAGAAG
....((((..(((((...(((....((((....(((((........((((((.((((....)))).))))))))))))))).)))...)))))..))))........ ( -27.50)
>DroSec_CAF1 8491 107 + 1
UAAAUGCCCAAGUGCAUAGCGUAAUUACUACUUCUCGCCGUAUUUAUACGAGAGGUACAAGUACUACUUGAAGCGAAAGUAUCUCAAGGUAUUCCGGCAGCCAGAAG
....((((..(((((.....(((.....(((((((((...........)))))))))....)))..(((((.((....))...))))))))))..))))........ ( -29.30)
>DroSim_CAF1 8891 107 + 1
UAAAUGCCCAAGUGCAUAGCGUAAUUACUACUUCUCGCCGUAUUUAUACGAGAGGUACAAGUACUACUUGAAGCGAAAGUAUCUCAAGGUAUUCCGGCAGCCAGAAG
....((((..(((((.....(((.....(((((((((...........)))))))))....)))..(((((.((....))...))))))))))..))))........ ( -29.30)
>DroEre_CAF1 8478 107 + 1
UAAAUGCCCAAGUGCAUAUCGUAAUUACUACUUCUCACCGUAUUUACUCGAUAGGCACAAGUACUGCUUGAAGCGAAAGUAUCUGAAGGUAUUCUGGCAGCCAGAAG
....((((...((((.((((((((.(((...........))).))))..)))).)))).((((((....((.((....)).))....))))))..))))........ ( -26.70)
>DroYak_CAF1 9374 107 + 1
UAAAUGCCCAAGUGCAUAUCGUAAUUACUACUUCUCACCGUAUUUAUUCGAGAGGUACAAGUACUACUUGAAGCGAAAGUAUCUCAAGGUAUUCUGGCAGCCAGAAG
....((((..(((((.....(((.....((((((((.............))))))))....)))..(((((.((....))...))))))))))..))))........ ( -27.32)
>consensus
UAAAUGCCCAAGUGCAUAGCGUAAUUACUACUUCUCGCCGUAUUUAUUCGAGAGGUACAAGUACUACUUGAAGCGAAAGUAUCUCAAGGUAUUCCGGCAGCCAGAAG
....((((..(((((.....(((.....((((((((.............))))))))....)))..(((((.((....))...))))))))))..))))........ (-23.92 = -24.40 +   0.48)

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 10:08:08 2006