Locus 5672

Sequence ID 3L_DroMel_CAF1
Location 15,559,405 – 15,559,557
Length 152
Max. P 0.997002
window8967 window8968 window8969

overview

Window 7

Location 15,559,405 – 15,559,522
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 93.50
Mean single sequence MFE -27.54
Consensus MFE -23.66
Energy contribution -23.86
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.86
SVM decision value 0.74
SVM RNA-class probability 0.837079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15559405 117 + 23771897
UUUAUCUUAGUUAUCCUUCUGAUUCUCCUCAGUCUUAGUCUUUGGCCAUACACAGUUAAUAGGCUAUUUGCACAAUUGCCUGGUGGACAAUUGCUGAUGGCCCAGGGAAAACUGUCU
.......(((((.(((((((((......))))...........((((((...(((.......((.....)).((((((((....)).))))))))))))))).))))).)))))... ( -30.20)
>DroSec_CAF1 21986 117 + 1
UUUGUGUUAUUUAUCCUUCUGAUUCUCCUCCGUCUUAGUCUUUGGCCAUACAUAGUUAAUAGGCUAUUUACACAAUUGCCUGGUGGACAAUUGCUGAUGGCCCAGGGAAAACUGUCU
.............(((((((((..(......)..)))).....((((((..((((((....))))))...((((((((((....)).)))))).)))))))).)))))......... ( -25.40)
>DroSim_CAF1 22433 117 + 1
UUUGUGUUAUUUAUCCUUCUGAUUCUCCUCCGUCUUAGUCUUUGGCCAUACAUAGUUAAUAGGCUAUUUACACAAUUGCCUGGUGGACAAUUGCUGAUGGCCCAGGGAAAACUGUCU
.............(((((((((..(......)..)))).....((((((..((((((....))))))...((((((((((....)).)))))).)))))))).)))))......... ( -25.40)
>DroEre_CAF1 22248 117 + 1
UCUAUAUUCCCUAUCCUUAUGAUUCCUCUCCUUCUUAGUCUUUGGCCAUAAAUAGUUAAUAGGCUAUUUACACAAUUGCCUGGUGGACAAUUGCUGAUGGCCCAGGGAAAACUGUCU
......((((((........((((............))))...((((((((((((((....)))))))).((((((((((....)).)))))).)))))))).))))))........ ( -30.50)
>DroYak_CAF1 42313 117 + 1
UUUAUAUUCCUUAUCCUUCUGAUUCUUCUGCUUCUUAGUCUUUGGCCAUACAUAGUUAAUAGGCUAUUUACACAAUUGCCUGGUGGACAAUUGCUGAUGGCCCAGGGAAAACUGUCU
......((((((.................(((....)))....((((((..((((((....))))))...((((((((((....)).)))))).)))))))).))))))........ ( -26.20)
>consensus
UUUAUAUUACUUAUCCUUCUGAUUCUCCUCCGUCUUAGUCUUUGGCCAUACAUAGUUAAUAGGCUAUUUACACAAUUGCCUGGUGGACAAUUGCUGAUGGCCCAGGGAAAACUGUCU
......................................(((((((((((..((((((....))))))...((((((((((....)).)))))).)))))).)))))))......... (-23.66 = -23.86 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,559,405 – 15,559,522
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 93.50
Mean single sequence MFE -28.26
Consensus MFE -22.44
Energy contribution -22.28
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.79
SVM decision value 0.58
SVM RNA-class probability 0.787845
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15559405 117 - 23771897
AGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGCAAAUAGCCUAUUAACUGUGUAUGGCCAAAGACUAAGACUGAGGAGAAUCAGAAGGAUAACUAAGAUAAA
....((((.(((...(((((((((((((((((.....)))))))))((.....))..........)).))))))...........((((......))))..))).))))........ ( -31.30)
>DroSec_CAF1 21986 117 - 1
AGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAAGACUAAGACGGAGGAGAAUCAGAAGGAUAAAUAACACAAA
.....(((((((((((((((((.(((((((((.....)))))))))....((((........))))).))))))...........))).)))))))..................... ( -26.70)
>DroSim_CAF1 22433 117 - 1
AGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAAGACUAAGACGGAGGAGAAUCAGAAGGAUAAAUAACACAAA
.....(((((((((((((((((.(((((((((.....)))))))))....((((........))))).))))))...........))).)))))))..................... ( -26.70)
>DroEre_CAF1 22248 117 - 1
AGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUUUAUGGCCAAAGACUAAGAAGGAGAGGAAUCAUAAGGAUAGGGAAUAUAGA
.....((.(((((((((((....(((((((((.....)))))))))((((((((........))))))))))))...............((....)).......))))))).))... ( -32.40)
>DroYak_CAF1 42313 117 - 1
AGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAAGACUAAGAAGCAGAAGAAUCAGAAGGAUAAGGAAUAUAAA
.....((.((((((((((((((.(((((((((.....)))))))))....((((........))))).)))))).....((....)))))....(((.....)))..)))).))... ( -24.20)
>consensus
AGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAAGACUAAGACGGAGGAGAAUCAGAAGGAUAAAUAACAUAAA
....((((((.....((((((..(((((((((.....)))))))))....((((........))))..)))))).)))))).................................... (-22.44 = -22.28 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,559,445 – 15,559,557
Length 112
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 96.29
Mean single sequence MFE -27.72
Consensus MFE -26.37
Energy contribution -26.21
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.95
SVM decision value 2.78
SVM RNA-class probability 0.997002
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15559445 112 - 23771897
CC---UCGCUCUUUUCUGCACUUAUCAGUAUUCGCAGCAGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGCAAAUAGCCUAUUAACUGUGUAUGGCCAAA
..---.........(((((.................)))))(((......)))(((((((((((((((((.....)))))))))((.....))..........)).))))))... ( -27.33)
>DroSec_CAF1 22026 112 - 1
GC---UCGCUCCUUUCUGCACUUAUCAGUAUUCGCAGCAGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAA
((---(.((......(((.......))).....)))))...(((......)))(((((((.(((((((((.....)))))))))....((((........))))).))))))... ( -27.50)
>DroSim_CAF1 22473 112 - 1
GC---UCGCUCUUUUCUGCACUUAUCAGUAUUCGCAGCAGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAA
((---(.((......(((.......))).....)))))...(((......)))(((((((.(((((((((.....)))))))))....((((........))))).))))))... ( -27.50)
>DroEre_CAF1 22288 112 - 1
CC---UCGCUCAUUUCUGCACUUAUCAGUAUUCGCAGCAGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUUUAUGGCCAAA
..---.........(((((.................)))))(((......)))((((....(((((((((.....)))))))))((((((((........))))))))))))... ( -29.43)
>DroYak_CAF1 42353 115 - 1
CCUUCUCUCUCAUUUCUGCACUUAUCAGUAUUCGCAGCAGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAA
..............(((((.................)))))(((......)))(((((((.(((((((((.....)))))))))....((((........))))).))))))... ( -26.83)
>consensus
CC___UCGCUCAUUUCUGCACUUAUCAGUAUUCGCAGCAGACAGUUUUCCCUGGGCCAUCAGCAAUUGUCCACCAGGCAAUUGUGUAAAUAGCCUAUUAACUAUGUAUGGCCAAA
..............(((((.................)))))(((......)))((((((..(((((((((.....)))))))))....((((........))))..))))))... (-26.37 = -26.21 +  -0.16)

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 11:56:14 2006