Locus 6023

Sequence ID 2R_DroMel_CAF1
Location 18,933,752 – 18,933,887
Length 135
Max. P 0.705746
window9656 window9657 window9658

overview

Window 6

Location 18,933,752 – 18,933,857
Length 105
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 87.52
Mean single sequence MFE -27.04
Consensus MFE -20.22
Energy contribution -20.02
Covariance contribution -0.20
Combinations/Pair 1.15
Mean z-score -1.55
Structure conservation index 0.75
SVM decision value 0.02
SVM RNA-class probability 0.543039
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18933752 105 - 20766785
AGCUAACAU----UCACAUUGCAAUUUUACUGAUAUUAUAACAGCCCGCGAGAUCUCUUACGCUGUUACAUGAACCGCGGGAAAGCAGAGAGUGAAAGAAGUGUAUUAU
.(((....(----((((.((((.......(((.........)))((((((.(.((................)).)))))))...))))...)))))...)))....... ( -20.29)
>DroSec_CAF1 32865 105 - 1
AGCUAACAU----UCACAUUGCAAUUUUGCUGAUAUUGUAACAGCACGCGAGAUCUCUUACGCUGUUACAUGAACCGCGGGAAAGCAGAGAGUGAAAGAAGUGUACUAU
.(((....(----((((.((((..((((((.(....(((((((((..(..((....))..))))))))))....).))))))..))))...)))))...)))....... ( -26.70)
>DroSim_CAF1 35860 105 - 1
AGCUAACAU----UCACAUUGCAAUUUUGCUGAUAUUGUAACAGCACGCGAGAUCUCUUACGCUGUUACAUGAACCGCGGGAAAGCAGAGAGUGAAAGAAGUGUACUAU
.(((....(----((((.((((..((((((.(....(((((((((..(..((....))..))))))))))....).))))))..))))...)))))...)))....... ( -26.70)
>DroEre_CAF1 33779 104 - 1
AGCUAACGU----ACACAUUGCAAUUUUGCU-AUAUUGUAACAGAACGAGCGAUCUCUUCCUCUGUUACAUGAACAGCGGAGAGGCUGAGAGUGAAAGAAGUGCACUUU
.((....))----......((((.(((..((-....(((((((((..(((......)))..)))))))))....((((......))))..))..)))....)))).... ( -26.80)
>DroYak_CAF1 34521 109 - 1
AUCCAACGUACGUACCCAUUGCAAUUUUGCUGAUAUUGUAACAGCUAGCGAGAUCUCUCACUCUGUUACAUUAACAGCGAGAAAGCAGAGAGUGAAAGAAGUGCACUAU
.......((((.(((.(.((((..((((((((.((.((((((((..((.(((....))).)))))))))).)).))))))))..)))).).)))......))))..... ( -34.70)
>consensus
AGCUAACAU____UCACAUUGCAAUUUUGCUGAUAUUGUAACAGCACGCGAGAUCUCUUACGCUGUUACAUGAACCGCGGGAAAGCAGAGAGUGAAAGAAGUGUACUAU
...................((((.(((((((.....(((((((((..(.(((....))).))))))))))......((......))....)))))))....)))).... (-20.22 = -20.02 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,933,781 – 18,933,887
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.32
Mean single sequence MFE -29.77
Consensus MFE -18.14
Energy contribution -18.02
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -2.25
Structure conservation index 0.61
SVM decision value 0.36
SVM RNA-class probability 0.705746
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18933781 106 + 20766785
CCGCGGUUCAUGUAACAGCGUAAGAGAUCUCGCGGGCUGUUAUAAUAUCAGUAAAAUUGCAAUGUGA----AUGUUAGCUGAUGCAAAAGAGAAAGGAGAGAGCAGGAAC----------
((...((((.(((((((((.(..((....))..).))))))))).(((((((.((....(.....).----...)).)))))))................)))).))...---------- ( -25.80)
>DroSec_CAF1 32894 106 + 1
CCGCGGUUCAUGUAACAGCGUAAGAGAUCUCGCGUGCUGUUACAAUAUCAGCAAAAUUGCAAUGUGA----AUGUUAGCUGAUGCAAAAGAGAAAGGAGAGAGCAGGAAG----------
((...((((.((((((((((...((....))...)))))))))).(((((((.((....(.....).----...)).)))))))................)))).))...---------- ( -29.00)
>DroSim_CAF1 35889 106 + 1
CCGCGGUUCAUGUAACAGCGUAAGAGAUCUCGCGUGCUGUUACAAUAUCAGCAAAAUUGCAAUGUGA----AUGUUAGCUGAUGCAAAAGAGAAUGGAGAGAGCAGGAAC----------
((...((((.((((((((((...((....))...)))))))))).(((((((.((....(.....).----...)).)))))))................)))).))...---------- ( -29.00)
>DroEre_CAF1 33808 113 + 1
CCGCUGUUCAUGUAACAGAGGAAGAGAUCGCUCGUUCUGUUACAAUAU-AGCAAAAUUGCAAUGUGU----ACGUUAGCUGAUGCAAAAGAGAAAGGAGGGAGCAAUAAC--UACUUUCG
..(((((...((((((((((...(((....))).))))))))))..))-)))....(((((..((..----......))...)))))....(((((.((..(....)..)--).))))). ( -32.30)
>DroYak_CAF1 34550 112 + 1
UCGCUGUUAAUGUAACAGAGUGAGAGAUCUCGCUAGCUGUUACAAUAUCAGCAAAAUUGCAAUGGGUACGUACGUUGGAUGUUGCAGAAGAGAAAGGAGAGAGCAAUAACUA--------
..((((.((.((((((((((((((....))))))..)))))))).)).)))).......(((((........)))))..((((((.................))))))....-------- ( -32.73)
>consensus
CCGCGGUUCAUGUAACAGCGUAAGAGAUCUCGCGUGCUGUUACAAUAUCAGCAAAAUUGCAAUGUGA____AUGUUAGCUGAUGCAAAAGAGAAAGGAGAGAGCAGGAAC__________
.....((((.(((((((((((.((....)).))..)))))))))......(((.....(((((((......))))).))...)))...............))))................ (-18.14 = -18.02 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,933,781 – 18,933,887
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.32
Mean single sequence MFE -22.46
Consensus MFE -15.98
Energy contribution -15.98
Covariance contribution 0.00
Combinations/Pair 1.18
Mean z-score -1.66
Structure conservation index 0.71
SVM decision value 0.09
SVM RNA-class probability 0.578530
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18933781 106 - 20766785
----------GUUCCUGCUCUCUCCUUUCUCUUUUGCAUCAGCUAACAU----UCACAUUGCAAUUUUACUGAUAUUAUAACAGCCCGCGAGAUCUCUUACGCUGUUACAUGAACCGCGG
----------....((((...................(((((.(((.((----((.....).))).))))))))....(((((((..(..((....))..))))))))........)))) ( -17.00)
>DroSec_CAF1 32894 106 - 1
----------CUUCCUGCUCUCUCCUUUCUCUUUUGCAUCAGCUAACAU----UCACAUUGCAAUUUUGCUGAUAUUGUAACAGCACGCGAGAUCUCUUACGCUGUUACAUGAACCGCGG
----------....((((...................((((((......----...............))))))..(((((((((..(..((....))..))))))))))......)))) ( -23.70)
>DroSim_CAF1 35889 106 - 1
----------GUUCCUGCUCUCUCCAUUCUCUUUUGCAUCAGCUAACAU----UCACAUUGCAAUUUUGCUGAUAUUGUAACAGCACGCGAGAUCUCUUACGCUGUUACAUGAACCGCGG
----------....((((...................((((((......----...............))))))..(((((((((..(..((....))..))))))))))......)))) ( -23.70)
>DroEre_CAF1 33808 113 - 1
CGAAAGUA--GUUAUUGCUCCCUCCUUUCUCUUUUGCAUCAGCUAACGU----ACACAUUGCAAUUUUGCU-AUAUUGUAACAGAACGAGCGAUCUCUUCCUCUGUUACAUGAACAGCGG
.(((((.(--(..........)).)))))....(((((...((....))----......)))))...((((-....(((((((((..(((......)))..))))))))).....)))). ( -22.80)
>DroYak_CAF1 34550 112 - 1
--------UAGUUAUUGCUCUCUCCUUUCUCUUCUGCAACAUCCAACGUACGUACCCAUUGCAAUUUUGCUGAUAUUGUAACAGCUAGCGAGAUCUCUCACUCUGUUACAUUAACAGCGA
--------..........................(((((......((....)).....)))))...((((((.((.((((((((..((.(((....))).)))))))))).)).)))))) ( -25.10)
>consensus
__________GUUCCUGCUCUCUCCUUUCUCUUUUGCAUCAGCUAACAU____UCACAUUGCAAUUUUGCUGAUAUUGUAACAGCACGCGAGAUCUCUUACGCUGUUACAUGAACCGCGG
..............((((...............(((((.....................)))))............(((((((((..(.(((....))).))))))))))......)))) (-15.98 = -15.98 +   0.00)

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 12:00:39 2006