Locus 4938

Sequence ID 2L_DroMel_CAF1
Location 14,157,941 – 14,158,135
Length 194
Max. P 0.999921
window7835 window7836 window7837 window7838

overview

Window 5

Location 14,157,941 – 14,158,058
Length 117
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 82.34
Mean single sequence MFE -62.43
Consensus MFE -42.11
Energy contribution -43.23
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -3.30
Structure conservation index 0.67
SVM decision value 2.07
SVM RNA-class probability 0.987320
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14157941 117 + 22407834
CCCAUCACGCACGCAGUUCCCGCUCCUGGAAGUGCGGUGGCCGCUGCUGCAGCCGCGGCUGCGGCCGCAGCGGUGGUCGCUGCCACAAGUUCCAGUGCCGGCGGCACCAGCACCACG
............((.....(((((((((((((((((((((((((((((((.(((((....))))).)))))))))))))))).)))...)))))).)..))))).....))...... ( -62.00)
>DroWil_CAF1 343715 117 + 1
CCCAUAACCCACGCAGUUCCAGCUCCUGGCAGUGCAGUGGCCGCGGCAGCAGCUGCUGCGGCUGCUGCAGCAGUUGCAGCUGCCACCAGCUCCGGAGCUGGAGGCACUAGCACUACA
............(((((((((((((((((((((((((..((((((((((...))))))))))..)))).((....)).)))))))........)))))))))...))).))...... ( -64.20)
>DroYak_CAF1 260968 117 + 1
CCCAUCACGCACGCGGUUCCCGCUCCUGGAAGUGCGGUGGCUGCUGCAGCAGCCGCGGCUGCGGCCGCAGCUGUAGUGGCUGCCACAAGUUCCACUGCCGGCGGGACCAGCACCACU
............(((((.((((((..(((((.(...(((((.((..(.(((((.(((((....))))).))))).)..)).))))).).))))).....))))))))).))...... ( -61.10)
>consensus
CCCAUCACGCACGCAGUUCCCGCUCCUGGAAGUGCGGUGGCCGCUGCAGCAGCCGCGGCUGCGGCCGCAGCAGUAGUAGCUGCCACAAGUUCCAGUGCCGGCGGCACCAGCACCACA
...........((((.((((.......)))).))))(((((.((.(((((.((.(((((....))))).)).))))).)).)))))........((((.((.....)).)))).... (-42.11 = -43.23 +   1.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,157,981 – 14,158,095
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 75.73
Mean single sequence MFE -60.93
Consensus MFE -42.49
Energy contribution -40.74
Covariance contribution -1.75
Combinations/Pair 1.42
Mean z-score -3.11
Structure conservation index 0.70
SVM decision value 4.56
SVM RNA-class probability 0.999921
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14157981 114 + 22407834
CCGCUGCUGCAGCCGCGGCUGCGGCCGCAGCGGUGGUCGCUGCCACAAGUUCCAGUGCCGGCGGCACCAGCACCACGGCUGCCGGCAAUGCCACAGCUACCUGCGGCAUGGGCG
((((((((((.(((((....))))).)))))))))).....(((...........((((((((((............))))))))))(((((.(((....))).))))).))). ( -65.50)
>DroWil_CAF1 343755 107 + 1
CCGCGGCAGCAGCUGCUGCGGCUGCUGCAGCAGUUGCAGCUGCCACCAGCUCCGGAGCUGGAGGCACUAGCACUACAACGGCUGGCAAUGCCACAGUGACUUGUGGU-------
(((((((.(((((((((((((...))))))))))))).)))))..((((((....)))))).))..(((((.(......))))))....(((((((....)))))))------- ( -55.30)
>DroYak_CAF1 261008 114 + 1
CUGCUGCAGCAGCCGCGGCUGCGGCCGCAGCUGUAGUGGCUGCCACAAGUUCCACUGCCGGCGGGACCAGCACCACUGCCGCCGGCAAUGCCACUGCUACCUGCGGCAUGGGCG
..(((...(((((....))))).(((((((..((((((((.......((.....))((((((((...(((.....)))))))))))...))))))))...)))))))...))). ( -62.00)
>consensus
CCGCUGCAGCAGCCGCGGCUGCGGCCGCAGCAGUAGUAGCUGCCACAAGUUCCAGUGCCGGCGGCACCAGCACCACAGCCGCCGGCAAUGCCACAGCUACCUGCGGCAUGGGCG
..((.(((((....))))).)).(((((((..(((((.(((......)))..((.(((((((((..............))))))))).)).....))))))))))))....... (-42.49 = -40.74 +  -1.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,157,981 – 14,158,095
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 75.73
Mean single sequence MFE -62.67
Consensus MFE -45.32
Energy contribution -47.33
Covariance contribution 2.01
Combinations/Pair 1.19
Mean z-score -2.99
Structure conservation index 0.72
SVM decision value 4.48
SVM RNA-class probability 0.999905
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14157981 114 - 22407834
CGCCCAUGCCGCAGGUAGCUGUGGCAUUGCCGGCAGCCGUGGUGCUGGUGCCGCCGGCACUGGAACUUGUGGCAGCGACCACCGCUGCGGCCGCAGCCGCGGCUGCAGCAGCGG
(((...((((((((((.((((((((...))).)))))...((((((((.....))))))))...))))))))))))).((.(.(((((((((((....))))))))))).).)) ( -68.80)
>DroWil_CAF1 343755 107 - 1
-------ACCACAAGUCACUGUGGCAUUGCCAGCCGUUGUAGUGCUAGUGCCUCCAGCUCCGGAGCUGGUGGCAGCUGCAACUGCUGCAGCAGCCGCAGCAGCUGCUGCCGCGG
-------...........((((((((.(((.(((.((((((((.....((((.((((((....)))))).)))))))))))).))))))(((((.......))))))))))))) ( -55.20)
>DroYak_CAF1 261008 114 - 1
CGCCCAUGCCGCAGGUAGCAGUGGCAUUGCCGGCGGCAGUGGUGCUGGUCCCGCCGGCAGUGGAACUUGUGGCAGCCACUACAGCUGCGGCCGCAGCCGCGGCUGCUGCAGCAG
......((((((((((.((....))((((((((((((((.....)))...)))))))))))...))))))))))((..(..((((((((((....))))))))))..)..)).. ( -64.00)
>consensus
CGCCCAUGCCGCAGGUAGCUGUGGCAUUGCCGGCAGCAGUGGUGCUGGUGCCGCCGGCACUGGAACUUGUGGCAGCCACAACAGCUGCGGCCGCAGCCGCGGCUGCUGCAGCGG
.....(((((((((....)))))))))(((((((((((((((((((((.....)))))..........((.(((((.......))))).))....)))))))))))))..))). (-45.32 = -47.33 +   2.01)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,158,018 – 14,158,135
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 83.19
Mean single sequence MFE -61.50
Consensus MFE -43.46
Energy contribution -44.10
Covariance contribution 0.64
Combinations/Pair 1.29
Mean z-score -1.64
Structure conservation index 0.71
SVM decision value 0.01
SVM RNA-class probability 0.540013
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14158018 117 - 22407834
GCGGCUGCCGCGCUGGUCAGUCCGGUGGCAUCCCCCACACCGCCCAUGCCGCAGGUAGCUGUGGCAUUGCCGGCAGCCGUGGUGCUGGUGCCGCCGGCACUGGAACUUGUGGCAGCG
...(((((((((....((((((((((((((((.(((((.(.(((.(((((((((....)))))))))....))).)..)))).)..))))))))))).)))))....))))))))). ( -69.10)
>DroSec_CAF1 246778 117 - 1
GCGGCUGCUGCGCUGGUCAGACCGGUAGCAUCCCCAACACCGCCCAUGCCGCAGGUAGCAGUGGCAUUGCCGGCGGCCGUGGUGCUGGUGCCGCCGGCACUGGAACUUGUGGCAGCC
..((((((..((....((((.((((..(((...(((.((((((....(((((.((((((....))..)))).))))).)))))).))))))..))))..))))....))..)))))) ( -61.40)
>DroSim_CAF1 243152 117 - 1
GCGGCUGCUGCGCUGGUCAGACCGGUAGCAUCCCCAACACCGCCCAUGCCGCAGGUAGCAGUGGCAUUGCCGGCGGCCGUGGUGCUGGUGCCGCCGGCACUGGAACUUGUGGCAGCC
..((((((..((....((((.((((..(((...(((.((((((....(((((.((((((....))..)))).))))).)))))).))))))..))))..))))....))..)))))) ( -61.40)
>DroYak_CAF1 261045 117 - 1
GCGGCUGCCGCGCUGGUCAGUCCGGUGGCAUCCCCCACGCCGCCCAUGCCGCAGGUAGCAGUGGCAUUGCCGGCGGCAGUGGUGCUGGUCCCGCCGGCAGUGGAACUUGUGGCAGCC
..((((((((((....(((.((((((((.(((.(((((((((((.(((((((........)))))))....)))))).)))).)..))).))))))).).)))....)))))))))) ( -66.20)
>DroAna_CAF1 241747 117 - 1
GCAGCCGCAACGCUGGUGAGUCCGGCGGCAUCCGCAGCUCCACCCACGCCGCAGGUGACGGUUGCGUUGCCAGCGGUCGUUGUGCUGGUUCCUCCGGCUCCUGAGCUGGUGGCAGCC
((.(((((..((((((.....)))))).......((((((.....(((((((.((..(((....)))..)).)))).)))...(((((.....)))))....))))))))))).)). ( -57.90)
>DroPer_CAF1 313577 117 - 1
GCGGCCGCCACAUUUGUGAGGCCGGUGGCAUCCGCGACUCCUGCUCCUCCGCAGGUGACGGUGGCAUUGCCCGCGGACGUGGUGCUCGUUCCGCCGGCACCAGAGCUGGUAGCAGCC
.(((((..(((....))).)))))((.((....)).))..(((((((..(...((((.((((((.((.((((((....)))).))..)).)))))).))))...)..)).))))).. ( -53.00)
>consensus
GCGGCUGCCGCGCUGGUCAGUCCGGUGGCAUCCCCAACACCGCCCAUGCCGCAGGUAGCAGUGGCAUUGCCGGCGGCCGUGGUGCUGGUGCCGCCGGCACUGGAACUUGUGGCAGCC
..((((((((((((((.....)))))....(((..............(((((.(((((........))))).)))))...((((((((.....)))))))))))....))))))))) (-43.46 = -44.10 +   0.64)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:33 2006