Locus 1219

Sequence ID 2L_DroMel_CAF1
Location 3,259,323 – 3,259,463
Length 140
Max. P 0.999933
window1995 window1996 window1997

overview

Window 5

Location 3,259,323 – 3,259,423
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.77
Mean single sequence MFE -27.61
Consensus MFE -21.18
Energy contribution -21.22
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.43
Structure conservation index 0.77
SVM decision value 0.02
SVM RNA-class probability 0.541752
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3259323 100 + 22407834
AAACAUGGCAUAUAGCAUGCA------UACACAC--------------ACAUUAAAUAUAGACCUAGUACGUGGCCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGU
.....((((...(((.(((((------....(((--------------((((.....)).((((((((.((.(....)))))))))))))))).....))))).)))))))......... ( -28.30)
>DroSec_CAF1 85899 106 + 1
AAACAUGGCAUAUAGCAUGCAGCGAUAUAUGUAU--------------ACAUUAAAUAUAGACCUAGUACGUGGCCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGU
.....((((.....((.....))...(((((((.--------------.......((((.((((((((.((.(....)))))))))))))))......)))))))..))))......... ( -26.64)
>DroSim_CAF1 89021 119 + 1
AAACAUGGCAUAUAGCAUGCAGCGAUAUAUGUAUGUACAUACACACACACAUUAAAUAUAGACCUAGUACGUGACCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACU-GU
.....((((.....(((((((........))))))).........(((((((.....)).((((((((.((.......)))))))))))))))..............))))......-.. ( -31.00)
>DroEre_CAF1 82740 107 + 1
AAACAUGGCAUAUAGCUGGUG-GGAUAU--------ACAUACAC----ACAUAUUAUAUAGACCUAGUACGUGUCCACCGACUGGGUCGUGUGACUUUUGCAUACUAGCCGGGAACUAGU
.....((((((((((...(((-......--------.......)----))...)))))).((((((((.((.(....)))))))))))(((((.(....))))))..))))......... ( -28.02)
>DroYak_CAF1 82111 108 + 1
AAACAUGGCAUGUAGCAGGAAUGUAUGU--------ACAUACAC----ACAUAUUAUAUAGACCUAGUACGUGUCCACCGACUGGAUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGU
.....((((..(((((((((((((.(((--------....))).----)))).((((((.((.(((((.((.(....)))))))).)))))))).)))))).)))..))))......... ( -24.10)
>consensus
AAACAUGGCAUAUAGCAUGCA_CGAUAUA___A___ACAUACAC____ACAUUAAAUAUAGACCUAGUACGUGGCCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGU
.....((((...................................................((((((((.((.(....)))))))))))(((((.(....))))))..))))......... (-21.18 = -21.22 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,259,351 – 3,259,463
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.32
Mean single sequence MFE -37.66
Consensus MFE -37.22
Energy contribution -36.94
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -2.33
Structure conservation index 0.99
SVM decision value 4.65
SVM RNA-class probability 0.999933
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3259351 112 + 22407834
--------ACAUUAAAUAUAGACCUAGUACGUGGCCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGUUGGUUAGUUUGCUGCCAAGUUUCCAGUCGAGUCACGCGCU
--------............((((((((.((.(....)))))))))))(((((((((..(((.(((((((((.......))))))))).)))......(........))))))))))... ( -37.70)
>DroSec_CAF1 85933 112 + 1
--------ACAUUAAAUAUAGACCUAGUACGUGGCCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGUUGGUUAGUUUGCUGCCAAGUUUCCAGUCGAGUCACGCGCU
--------............((((((((.((.(....)))))))))))(((((((((..(((.(((((((((.......))))))))).)))......(........))))))))))... ( -37.70)
>DroSim_CAF1 89061 119 + 1
ACACACACACAUUAAAUAUAGACCUAGUACGUGACCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACU-GUUGGUUAGUUUGCUGCCAAGUUUCCAGUCGAGUCACGCGCU
.........................((..((((((...((((((((......(((((..(((.(((((((((.....-.))))))))).)))....))))))))))))).))))))..)) ( -37.60)
>DroEre_CAF1 82771 116 + 1
ACAC----ACAUAUUAUAUAGACCUAGUACGUGUCCACCGACUGGGUCGUGUGACUUUUGCAUACUAGCCGGGAACUAGUUGGCUAGUUUGCUGCCAAGUUUCUAGUCGAGUCACGCGCU
....----............((((((((.((.(....)))))))))))(((((((((..(((.(((((((((.......))))))))).)))......(........))))))))))... ( -41.20)
>DroYak_CAF1 82143 116 + 1
ACAC----ACAUAUUAUAUAGACCUAGUACGUGUCCACCGACUGGAUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGUUGGUUAGUUUGCUGCCAAGUUUCCAGUCGAGUCACGCGCU
....----.................((..((((.(...((((((((......(((((..(((.(((((((((.......))))))))).)))....))))))))))))).).))))..)) ( -34.10)
>consensus
ACAC____ACAUUAAAUAUAGACCUAGUACGUGGCCACCGACUGGGUCGUGUGACUUUUGCAUAUUAGCCGAGAACUAGUUGGUUAGUUUGCUGCCAAGUUUCCAGUCGAGUCACGCGCU
....................((((((((.((.(....)))))))))))(((((((((..(((.(((((((((.......))))))))).)))......(........))))))))))... (-37.22 = -36.94 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,259,351 – 3,259,463
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.32
Mean single sequence MFE -32.88
Consensus MFE -27.52
Energy contribution -27.60
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.41
Structure conservation index 0.84
SVM decision value 0.39
SVM RNA-class probability 0.716636
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3259351 112 - 22407834
AGCGCGUGACUCGACUGGAAACUUGGCAGCAAACUAACCAACUAGUUCUCGGCUAAUAUGCAAAAGUCACACGACCCAGUCGGUGGCCACGUACUAGGUCUAUAUUUAAUGU--------
((..((((.(((((((((....(((((.(..(((((......)))))..).))))).........(((....))))))))))).)..))))..)).................-------- ( -30.20)
>DroSec_CAF1 85933 112 - 1
AGCGCGUGACUCGACUGGAAACUUGGCAGCAAACUAACCAACUAGUUCUCGGCUAAUAUGCAAAAGUCACACGACCCAGUCGGUGGCCACGUACUAGGUCUAUAUUUAAUGU--------
((..((((.(((((((((....(((((.(..(((((......)))))..).))))).........(((....))))))))))).)..))))..)).................-------- ( -30.20)
>DroSim_CAF1 89061 119 - 1
AGCGCGUGACUCGACUGGAAACUUGGCAGCAAACUAACCAAC-AGUUCUCGGCUAAUAUGCAAAAGUCACACGACCCAGUCGGUGGUCACGUACUAGGUCUAUAUUUAAUGUGUGUGUGU
((..((((((((((((((....(((((.(..((((.......-))))..).))))).........(((....))))))))))..)))))))..)).....(((((.....)))))..... ( -32.60)
>DroEre_CAF1 82771 116 - 1
AGCGCGUGACUCGACUAGAAACUUGGCAGCAAACUAGCCAACUAGUUCCCGGCUAGUAUGCAAAAGUCACACGACCCAGUCGGUGGACACGUACUAGGUCUAUAUAAUAUGU----GUGU
.((((((((((.(.((((....))))).(((.(((((((...........))))))).)))...))))))..((((.(((((.......)).))).))))..........))----)).. ( -37.60)
>DroYak_CAF1 82143 116 - 1
AGCGCGUGACUCGACUGGAAACUUGGCAGCAAACUAACCAACUAGUUCUCGGCUAAUAUGCAAAAGUCACACGAUCCAGUCGGUGGACACGUACUAGGUCUAUAUAAUAUGU----GUGU
.(((((((...((((((((....((((.(..(((((......)))))..).((......))....)))).....))))))))((((((.(......)))))))....)))))----)).. ( -33.80)
>consensus
AGCGCGUGACUCGACUGGAAACUUGGCAGCAAACUAACCAACUAGUUCUCGGCUAAUAUGCAAAAGUCACACGACCCAGUCGGUGGACACGUACUAGGUCUAUAUUUAAUGU____GUGU
((..((((.(((((((((....(((((.(..(((((......)))))..).))))).........(((....))))))))))).)..))))..))......................... (-27.52 = -27.60 +   0.08)

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 09:56:57 2006