Locus 9014

Sequence ID 3R_DroMel_CAF1
Location 24,160,812 – 24,160,945
Length 133
Max. P 0.986743
window14440 window14441 window14442

overview

Window 0

Location 24,160,812 – 24,160,925
Length 113
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 90.94
Mean single sequence MFE -37.03
Consensus MFE -34.25
Energy contribution -35.37
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -2.56
Structure conservation index 0.92
SVM decision value 1.59
SVM RNA-class probability 0.965995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24160812 113 + 27905053
CCCAGCUUUACUGUGCCUACUAGGAUUUUCCAACAAGAUUGCGAGUUGGGCGAACGCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC-UUCUGCAAUAA
....((........))......((.....))......(((((.((..((((((((..(((((....((((((.......))))))..)))))..))))))))-..))))))).. ( -36.30)
>DroEre_CAF1 14445 114 + 1
CCGAGCUUUACUGUGCCUACCAGGAUUUUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCCCAAUUACUGCGAUUAAUCUCAAGUUCGCCCCUCCUGCAAUAC
....((........))(((...((.....))...)))((((((.((.(((((((((.(((((....(((((.........)))))..))))).))))))))).)).)))))).. ( -38.00)
>DroYak_CAF1 18133 114 + 1
CCGAGCUCUACUGUGCCUGCUAGGAUUUUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACAGUGAUUAAUCUCAAGUUCGCCCCUCCUGCAUAAA
((.(((............))).))...............((((.((.(((((((((.(((((....((..((.......))..))..))))).))))))))).)).)))).... ( -36.80)
>consensus
CCGAGCUUUACUGUGCCUACUAGGAUUUUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACAGCGAUUAAUCUCAAGUUCGCCCCUCCUGCAAUAA
....((........))......((.....))......((((((.((.(((((((((.(((((....((((((.......))))))..))))).))))))))).)).)))))).. (-34.25 = -35.37 +   1.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 24,160,852 – 24,160,945
Length 93
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 89.57
Mean single sequence MFE -31.70
Consensus MFE -30.45
Energy contribution -30.90
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -4.46
Structure conservation index 0.96
SVM decision value 2.05
SVM RNA-class probability 0.986743
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24160852 93 + 27905053
GCGAGUUGGGCGAACGCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC-UUCUGCAAUAAUAUUUACAUCUUUACUUAAU
((.((..((((((((..(((((....((((((.......))))))..)))))..))))))))-..))))......................... ( -30.80)
>DroEre_CAF1 14485 90 + 1
GCGAGAUGGGCGAACUCGAGGUGUUUGUUGCCCAAUUACUGCGAUUAAUCUCAAGUUCGCCCCUCCUGCAAUACUAUUUA----UUUACUUAAU
(((.((.(((((((((.(((((....(((((.........)))))..))))).))))))))).)).)))...........----.......... ( -32.30)
>DroYak_CAF1 18173 90 + 1
GCGAGAUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACAGUGAUUAAUCUCAAGUUCGCCCCUCCUGCAUAAAUAUUUA----UUUACUUAAU
(((.((.(((((((((.(((((....((..((.......))..))..))))).))))))))).)).)))...........----.......... ( -32.00)
>consensus
GCGAGAUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACAGCGAUUAAUCUCAAGUUCGCCCCUCCUGCAAUAAUAUUUA____UUUACUUAAU
(((.((.(((((((((.(((((....((((((.......))))))..))))).))))))))).)).)))......................... (-30.45 = -30.90 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 24,160,852 – 24,160,945
Length 93
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 89.57
Mean single sequence MFE -27.11
Consensus MFE -23.21
Energy contribution -24.21
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.24
Structure conservation index 0.86
SVM decision value 1.55
SVM RNA-class probability 0.963539
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24160852 93 - 27905053
AUUAAGUAAAGAUGUAAAUAUUAUUGCAGAA-GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGCGUUCGCCCAACUCGC
.....((((.((((....)))).))))....-((((((((.((((.......((((....)).)).........)))).))))))))....... ( -23.09)
>DroEre_CAF1 14485 90 - 1
AUUAAGUAAA----UAAAUAGUAUUGCAGGAGGGGCGAACUUGAGAUUAAUCGCAGUAAUUGGGCAACAAACACCUCGAGUUCGCCCAUCUCGC
..........----...........((..((.(((((((((((((........(((...)))(....)......))))))))))))).))..)) ( -28.80)
>DroYak_CAF1 18173 90 - 1
AUUAAGUAAA----UAAAUAUUUAUGCAGGAGGGGCGAACUUGAGAUUAAUCACUGUAAUUGAGCAACAAACACCUCGAGUUCGCCCAUCUCGC
.....(((((----(....))))))((..((.(((((((((((((.........(((......)))........))))))))))))).))..)) ( -29.43)
>consensus
AUUAAGUAAA____UAAAUAUUAUUGCAGGAGGGGCGAACUUGAGAUUAAUCGCAGUAAUUGAGCAACAAACACCUCGAGUUCGCCCAUCUCGC
.........................((.(((.(((((((((((((..........((......)).........))))))))))))).))).)) (-23.21 = -24.21 +   1.00)

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 13:24:47 2006