Locus 2962

Sequence ID 3R_DroMel_CAF1
Location 7,920,377 – 7,920,476
Length 99
Max. P 0.999495
window4763 window4764

overview

Window 3

Location 7,920,377 – 7,920,476
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 93.94
Mean single sequence MFE -32.00
Consensus MFE -31.18
Energy contribution -30.94
Covariance contribution -0.24
Combinations/Pair 1.17
Mean z-score -1.99
Structure conservation index 0.97
SVM decision value 3.66
SVM RNA-class probability 0.999495
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7920377 99 + 27905053
CAGCCGGCAAAUAACCCGACGGUUCGAUUCCGAAAAUUCAGUGCAACCAGAGGGAUGUGAACGGCACAAAGCUGGGGAAGUUGGAAACGAACCGGUAUG
....(((........))).(((((((.((((((...(((...(((.((....)).)))...((((.....))))..))).)))))).)))))))..... ( -31.90)
>DroSec_CAF1 51705 98 + 1
CAGCCGGCAAAUAUCCCGACGGUUCGAUUCCGAAAAUUCAGUGCAACCCGAG-GAUGUGAACGGCACAAAGCUGGGGAAGUUGGAAACGAACCGGUAUG
....(((........))).(((((((.((((((...(((...(((.((...)-).)))...((((.....))))..))).)))))).)))))))..... ( -30.40)
>DroSim_CAF1 53467 99 + 1
CAGCCGGCAAAUAACCCGACGGUUCGAUUCCGAAAAUUCAGUGCAACCCGAGGGAUGUGAACGGCACAAAGCUGGGGAAGUUGGAAACGAACCGGCAUG
..(((((........))...((((((.((((((...(((...(((.((....)).)))...((((.....))))..))).)))))).)))))))))... ( -35.40)
>DroEre_CAF1 52244 99 + 1
CAGCCGGCAAACAACCCGACGGUUCGAUUCCAGAAAUUCAGUGCAACCGGAGGGAUGCGAACAGCACAAAGCUGGGGAAGUUUGAAACGAACCGGUAUG
....(((........))).(((((((.(((.(((..(((..((((.((....)).))))..((((.....)))).)))..)))))).)))))))..... ( -29.30)
>DroYak_CAF1 52851 99 + 1
CAGCCGGCAAACAAACCGACGGUUCGAUUCCGAAAAUUCAGUGCAACCAGAGGGAUGCGAACGGCACAAAGCUGGGGAAGUGGGAAACGAACCGGUAUC
....(((........))).(((((((.((((.(...(((..((((.((....)).))))..((((.....))))..))).).)))).)))))))..... ( -33.00)
>consensus
CAGCCGGCAAAUAACCCGACGGUUCGAUUCCGAAAAUUCAGUGCAACCAGAGGGAUGUGAACGGCACAAAGCUGGGGAAGUUGGAAACGAACCGGUAUG
..(((((........))...((((((.((((((...(((...(((.((....)).)))...((((.....))))..))).)))))).)))))))))... (-31.18 = -30.94 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,920,377 – 7,920,476
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 93.94
Mean single sequence MFE -30.00
Consensus MFE -24.66
Energy contribution -24.82
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.82
SVM decision value 0.43
SVM RNA-class probability 0.734788
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7920377 99 - 27905053
CAUACCGGUUCGUUUCCAACUUCCCCAGCUUUGUGCCGUUCACAUCCCUCUGGUUGCACUGAAUUUUCGGAAUCGAACCGUCGGGUUAUUUGCCGGCUG
......((((((.((((.......((((...((((.....)))).....)))).......((....)))))).))))))(((((........))))).. ( -28.40)
>DroSec_CAF1 51705 98 - 1
CAUACCGGUUCGUUUCCAACUUCCCCAGCUUUGUGCCGUUCACAUC-CUCGGGUUGCACUGAAUUUUCGGAAUCGAACCGUCGGGAUAUUUGCCGGCUG
......((((((.((((.....(((.((...((((.....))))..-)).))).......((....)))))).))))))(((((.(....).))))).. ( -30.00)
>DroSim_CAF1 53467 99 - 1
CAUGCCGGUUCGUUUCCAACUUCCCCAGCUUUGUGCCGUUCACAUCCCUCGGGUUGCACUGAAUUUUCGGAAUCGAACCGUCGGGUUAUUUGCCGGCUG
...(((((((((.((((.....(((.((...((((.....))))...)).))).......((....)))))).))))))....(((.....)))))).. ( -30.60)
>DroEre_CAF1 52244 99 - 1
CAUACCGGUUCGUUUCAAACUUCCCCAGCUUUGUGCUGUUCGCAUCCCUCCGGUUGCACUGAAUUUCUGGAAUCGAACCGUCGGGUUGUUUGCCGGCUG
......(((((((((((((.(((..((((.....))))...(((.((....)).)))...))).)).))))).))))))(((((........))))).. ( -30.20)
>DroYak_CAF1 52851 99 - 1
GAUACCGGUUCGUUUCCCACUUCCCCAGCUUUGUGCCGUUCGCAUCCCUCUGGUUGCACUGAAUUUUCGGAAUCGAACCGUCGGUUUGUUUGCCGGCUG
......((((((.((((.......((((....((((.....))))....)))).......((....)))))).))))))((((((......)))))).. ( -30.80)
>consensus
CAUACCGGUUCGUUUCCAACUUCCCCAGCUUUGUGCCGUUCACAUCCCUCGGGUUGCACUGAAUUUUCGGAAUCGAACCGUCGGGUUAUUUGCCGGCUG
......((((((.((((..........((.....)).(((((((.((....)).))...)))))....)))).))))))(((((........))))).. (-24.66 = -24.82 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:48 2006