Locus 1435

Sequence ID 3L_DroMel_CAF1
Location 4,153,479 – 4,153,635
Length 156
Max. P 0.994603
window2233 window2234 window2235 window2236

overview

Window 3

Location 4,153,479 – 4,153,595
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -27.29
Consensus MFE -18.22
Energy contribution -17.78
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -2.43
Structure conservation index 0.67
SVM decision value 1.83
SVM RNA-class probability 0.979064
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153479 116 + 23771897
---UCUCAUUCUGCUAAUUCAAAUCGAGCGGU-UUUAUUUCUGUUCUCCAUAACGCGAUCUGGCAACCUCUUCCCUUAAAAUGUUUCAUCCCUGGGAAGAGGGUUGCCUCUGCUUCAAAA
---......................((((((.-.......))))))........(((....((((((((((((((..................))))))).)))))))..)))....... ( -32.47)
>DroSim_CAF1 3063 116 + 1
UGUUCUCAUUUUACCAAUUCAAAUCGAGCGGUCUUUACUAUUUUACUUUAUAACGCGAUCUGGCAACCUCUUCCCUU----UGUUUCAUCCCUGGAAUGAGGGUUGCCUCUGCUUCAAAU
.........................((((((((.......................)))).((((((((.......(----..(((((....)))))..)))))))))...))))..... ( -20.51)
>DroYak_CAF1 3249 120 + 1
UGUACUUUUCGUACAAAUUCAAAUCAAGCGGUCUUUACGCUUGUUCCUUAUACCGCGAUCUGGCAACCUCUUCUUUUAAAAUGCUUCAUCCCUGGAAAGAGGGUUGCCCUUUCUUCAAUU
(((((.....))))).........((((((.......)))))).............((...((((((((..((((((...(((...))).....))))))))))))))...))....... ( -28.90)
>consensus
UGUUCUCAUUCUACAAAUUCAAAUCGAGCGGUCUUUACUAUUGUUCUUUAUAACGCGAUCUGGCAACCUCUUCCCUUAAAAUGUUUCAUCCCUGGAAAGAGGGUUGCCUCUGCUUCAAAU
...........................(((.......................))).....(((((((((((((...................)))).)).)))))))............ (-18.22 = -17.78 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,153,479 – 4,153,595
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.17
Mean single sequence MFE -29.04
Consensus MFE -21.52
Energy contribution -23.30
Covariance contribution 1.78
Combinations/Pair 1.04
Mean z-score -1.70
Structure conservation index 0.74
SVM decision value 0.70
SVM RNA-class probability 0.828051
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153479 116 - 23771897
UUUUGAAGCAGAGGCAACCCUCUUCCCAGGGAUGAAACAUUUUAAGGGAAGAGGUUGCCAGAUCGCGUUAUGGAGAACAGAAAUAAA-ACCGCUCGAUUUGAAUUAGCAGAAUGAGA---
.......((...(((((((.(((((((.((((((...))))))..))))))))))))))((((((.((...((..............-.)))).))))))......)).........--- ( -33.56)
>DroSim_CAF1 3063 116 - 1
AUUUGAAGCAGAGGCAACCCUCAUUCCAGGGAUGAAACA----AAGGGAAGAGGUUGCCAGAUCGCGUUAUAAAGUAAAAUAGUAAAGACCGCUCGAUUUGAAUUGGUAAAAUGAGAACA
..(..(..(((((((((((.((.((((..(.......).----...))))))))))))).((.((.(((..................))))).))..))))..)..)............. ( -22.87)
>DroYak_CAF1 3249 120 - 1
AAUUGAAGAAAGGGCAACCCUCUUUCCAGGGAUGAAGCAUUUUAAAAGAAGAGGUUGCCAGAUCGCGGUAUAAGGAACAAGCGUAAAGACCGCUUGAUUUGAAUUUGUACGAAAAGUACA
..(..((((...(((((((.(((((...((((((...))))))....))))))))))))...)).............((((((.......)))))).))..)...(((((.....))))) ( -30.70)
>consensus
AUUUGAAGCAGAGGCAACCCUCUUUCCAGGGAUGAAACAUUUUAAGGGAAGAGGUUGCCAGAUCGCGUUAUAAAGAACAAAAGUAAAGACCGCUCGAUUUGAAUUAGUAAAAUGAGAACA
............(((((((.(((((((..(((((...)))))...))))))))))))))((((((((.......................)))..))))).................... (-21.52 = -23.30 +   1.78)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,153,515 – 4,153,635
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.25
Mean single sequence MFE -27.51
Consensus MFE -18.72
Energy contribution -18.61
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -2.41
Structure conservation index 0.68
SVM decision value 2.49
SVM RNA-class probability 0.994603
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153515 120 + 23771897
CUGUUCUCCAUAACGCGAUCUGGCAACCUCUUCCCUUAAAAUGUUUCAUCCCUGGGAAGAGGGUUGCCUCUGCUUCAAAAAAAUGGCGCGAAAUUUCAACAUAUCGUAAAUUCAAUAUAA
..............(((((..((((((((((((((..................))))))).)))))))..(((.(((......))).)))............)))))............. ( -30.67)
>DroSim_CAF1 3103 112 + 1
UUUUACUUUAUAACGCGAUCUGGCAACCUCUUCCCUU----UGUUUCAUCCCUGGAAUGAGGGUUGCCUCUGCUUCAAAUAAGUGGCGCGAAAUUUCAACAUAUCGUCAG----AUAUAA
.............((((....((((((((.......(----..(((((....)))))..))))))))).(..(((.....)))..)))))..........(((((....)----)))).. ( -27.71)
>DroYak_CAF1 3289 107 + 1
UUGUUCCUUAUACCGCGAUCUGGCAACCUCUUCUUUUAAAAUGCUUCAUCCCUGGAAAGAGGGUUGCCCUUUCUUCAAUUAUUUGGCGCAAAAUUUGAACAUAUCAU-------------
.(((((.......(((((...((((((((..((((((...(((...))).....))))))))))))))...))..(((....))))))........)))))......------------- ( -24.16)
>consensus
UUGUUCUUUAUAACGCGAUCUGGCAACCUCUUCCCUUAAAAUGUUUCAUCCCUGGAAAGAGGGUUGCCUCUGCUUCAAAUAAAUGGCGCGAAAUUUCAACAUAUCGU_A_____AUAUAA
.............((((....(((((((((((((...................)))).)).)))))))......(((......))))))).............................. (-18.72 = -18.61 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,153,515 – 4,153,635
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -29.37
Consensus MFE -21.64
Energy contribution -23.20
Covariance contribution 1.56
Combinations/Pair 1.08
Mean z-score -1.70
Structure conservation index 0.74
SVM decision value 1.07
SVM RNA-class probability 0.909879
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4153515 120 - 23771897
UUAUAUUGAAUUUACGAUAUGUUGAAAUUUCGCGCCAUUUUUUUGAAGCAGAGGCAACCCUCUUCCCAGGGAUGAAACAUUUUAAGGGAAGAGGUUGCCAGAUCGCGUUAUGGAGAACAG
..((((((......))))))(((...((..(((((((......))..))...(((((((.(((((((.((((((...))))))..)))))))))))))).....)))..))....))).. ( -34.90)
>DroSim_CAF1 3103 112 - 1
UUAUAU----CUGACGAUAUGUUGAAAUUUCGCGCCACUUAUUUGAAGCAGAGGCAACCCUCAUUCCAGGGAUGAAACA----AAGGGAAGAGGUUGCCAGAUCGCGUUAUAAAGUAAAA
.(((((----(....)))))).....((..(((((..(......)..))...(((((((.((.((((..(.......).----...))))))))))))).....)))..))......... ( -26.60)
>DroYak_CAF1 3289 107 - 1
-------------AUGAUAUGUUCAAAUUUUGCGCCAAAUAAUUGAAGAAAGGGCAACCCUCUUUCCAGGGAUGAAGCAUUUUAAAAGAAGAGGUUGCCAGAUCGCGGUAUAAGGAACAA
-------------......(((((.....((((..(((....)))..((...(((((((.(((((...((((((...))))))....))))))))))))...))))))......))))). ( -26.60)
>consensus
UUAUAU_____U_ACGAUAUGUUGAAAUUUCGCGCCAAUUAUUUGAAGCAGAGGCAACCCUCUUUCCAGGGAUGAAACAUUUUAAGGGAAGAGGUUGCCAGAUCGCGUUAUAAAGAACAA
..............................((((.((......)).......(((((((.(((((((..(((((...)))))...))))))))))))))....))))............. (-21.64 = -23.20 +   1.56)

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 10:07:33 2006