Locus 1093

Sequence ID 3R_DroMel_CAF1
Location 3,309,112 – 3,309,284
Length 172
Max. P 0.983097
window1784 window1785 window1786 window1787

overview

Window 4

Location 3,309,112 – 3,309,204
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 88.38
Mean single sequence MFE -24.20
Consensus MFE -16.98
Energy contribution -17.47
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.70
SVM decision value 0.37
SVM RNA-class probability 0.709898
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3309112 92 + 27905053
AGUGCAGAAUCAAGGAUCUUGAGGCCAUGGAGCUGAAGCCUGGAGCUGGAGCACCAACGCCACAUAAAUUGCGGCGCCCAAAAUGCAUAAAC
.(((((...(((((...)))))(((..(((.(((..(((.....)))..))).)))..(((.((.....)).)))))).....))))).... ( -29.70)
>DroSec_CAF1 13323 79 + 1
AGUGCAGAAUCAAGGAUCUUGAGGCCAUGGA-------------GCUGGAGCACCAACGCCACAUAAAUUGCGGCGCCCAAAAUGCAUAAAC
.(((((...(((((...)))))(((..(((.-------------((....)).)))..(((.((.....)).)))))).....))))).... ( -23.90)
>DroSim_CAF1 17574 79 + 1
AGUGCAGAAUCAAGGAUCUUGAGGCCAUGGA-------------GCUGGAGCACCAACGCCACAUAAAUUGCGGCGCCCAAAAUGCAUAAAC
.(((((...(((((...)))))(((..(((.-------------((....)).)))..(((.((.....)).)))))).....))))).... ( -23.90)
>DroYak_CAF1 23602 85 + 1
AGUGCAGAACCAAGAAUCUUGAGGCCAUGGAGCC-------GGAGCCGGAGCACCAACGCCACAUAAAUUGCGACGCCCAAAAUGCAUAAAG
.(((((....((((...)))).(((..(((..((-------(....)))....))).(((..........)))..))).....))))).... ( -19.30)
>consensus
AGUGCAGAAUCAAGGAUCUUGAGGCCAUGGA_____________GCUGGAGCACCAACGCCACAUAAAUUGCGGCGCCCAAAAUGCAUAAAC
.((((((..(((((...)))))..)..(((..............((....)).....((((.((.....)).)))).)))...))))).... (-16.98 = -17.47 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,309,112 – 3,309,204
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 88.38
Mean single sequence MFE -26.98
Consensus MFE -24.66
Energy contribution -24.10
Covariance contribution -0.56
Combinations/Pair 1.13
Mean z-score -1.91
Structure conservation index 0.91
SVM decision value 1.30
SVM RNA-class probability 0.939045
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3309112 92 - 27905053
GUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGCUCCAGGCUUCAGCUCCAUGGCCUCAAGAUCCUUGAUUCUGCACU
.....((((.....(((((((((.....))))))..(((.(((..(((.....)))..))).)))..)))(((((...)))))...)))).. ( -30.30)
>DroSec_CAF1 13323 79 - 1
GUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGC-------------UCCAUGGCCUCAAGAUCCUUGAUUCUGCACU
.....((((.....(((((((((.....))))))(((((....)))))-------------......)))(((((...)))))...)))).. ( -25.80)
>DroSim_CAF1 17574 79 - 1
GUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGC-------------UCCAUGGCCUCAAGAUCCUUGAUUCUGCACU
.....((((.....(((((((((.....))))))(((((....)))))-------------......)))(((((...)))))...)))).. ( -25.80)
>DroYak_CAF1 23602 85 - 1
CUUUAUGCAUUUUGGGCGUCGCAAUUUAUGUGGCGUUGGUGCUCCGGCUCC-------GGCUCCAUGGCCUCAAGAUUCUUGGUUCUGCACU
.....((((((((((((((((((.....))))))(((((.((....)).))-------)))......))).)))))..........)))).. ( -26.00)
>consensus
GUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGC_____________UCCAUGGCCUCAAGAUCCUUGAUUCUGCACU
.....((((.....(((((((((.....))))))(((((....)))))...................)))(((((...)))))...)))).. (-24.66 = -24.10 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,309,124 – 3,309,244
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.63
Mean single sequence MFE -46.60
Consensus MFE -39.79
Energy contribution -40.85
Covariance contribution 1.06
Combinations/Pair 1.09
Mean z-score -2.82
Structure conservation index 0.85
SVM decision value 1.93
SVM RNA-class probability 0.983097
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3309124 120 - 27905053
GGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGCUCCAGGCUUCAGCUCCAUGGCCUCAAGAUCCU
(((((.(((((.(((((((..((...((.(((.((((.........)))).))).))((((((.....))))))(((((....)))))..))...)))))))))))))))))........ ( -52.50)
>DroSec_CAF1 13335 107 - 1
GGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGC-------------UCCAUGGCCUCAAGAUCCU
(((((.(((((.(((((.........((.(((.((((.........)))).))).))((((((.....))))))..........))))-------------)))))))))))........ ( -44.20)
>DroSim_CAF1 17586 107 - 1
GGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGC-------------UCCAUGGCCUCAAGAUCCU
(((((.(((((.(((((.........((.(((.((((.........)))).))).))((((((.....))))))..........))))-------------)))))))))))........ ( -44.20)
>DroYak_CAF1 23614 113 - 1
GGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGCUUUAUGCAUUUUGGGCGUCGCAAUUUAUGUGGCGUUGGUGCUCCGGCUCC-------GGCUCCAUGGCCUCAAGAUUCU
(((((.(((((.(((((.........((.(((.((((.........)))).))).))((((((.....))))))(((((....)))))..)-------))))))))))))))........ ( -45.50)
>consensus
GGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGUGCUCCAGC_____________UCCAUGGCCUCAAGAUCCU
(((((.(((((.((((..........((.(((.((((.........)))).))).))((((((.....))))))(((((....)))))..........))))))))))))))........ (-39.79 = -40.85 +   1.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,309,164 – 3,309,284
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.20
Mean single sequence MFE -46.05
Consensus MFE -43.28
Energy contribution -43.15
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -2.75
Structure conservation index 0.94
SVM decision value 1.89
SVM RNA-class probability 0.981628
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3309164 120 - 27905053
UCCUUCCUUGCUUCCCCAUAAAGUGCCCGAAAUGUAUGCUGGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGU
...............(((......(((((((((((((((..((.((.((.((.((...........)))).)).))))..))..)))))))))))))((((((.....))))))..))). ( -44.30)
>DroSec_CAF1 13362 117 - 1
UCCUUCCUUGC---CCCAUAAAGUGCCCGAAAUGUAUGCCGGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGU
.....((.(((---(.(((((((((((((((((((((((((((.((.((.((.((...........)))).)).))))))))..))))))))))))))).....)))))).))))..)). ( -48.20)
>DroSim_CAF1 17613 117 - 1
UCCUUCCUUGC---CCCAUAAAGUGCCCGAAAUGUAUGCCGGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGU
.....((.(((---(.(((((((((((((((((((((((((((.((.((.((.((...........)))).)).))))))))..))))))))))))))).....)))))).))))..)). ( -48.20)
>DroYak_CAF1 23647 117 - 1
UCCUCUCUCGC---CCCAUAAAGUGCCCGAAAUGUAUGCCGGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGCUUUAUGCAUUUUGGGCGUCGCAAUUUAUGUGGCGUUGGU
....((..(((---(.((((((.(((((((((((((((..((((((.((.((.((...........)))).)).))))).)..)))))))))))))))......)))))).))))..)). ( -43.50)
>consensus
UCCUUCCUUGC___CCCAUAAAGUGCCCGAAAUGUAUGCCGGGGCACGUGGCAGCUGAAAAUGAUUGCGCGACAUGCUUGGUUUAUGCAUUUUGGGCGCCGCAAUUUAUGUGGCGUUGGU
...............(((......(((((((((((((((((((.((.((.((.((...........)))).)).))))))))..)))))))))))))((((((.....))))))..))). (-43.28 = -43.15 +  -0.13)

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 10:00:40 2006