Locus 4704

Sequence ID 2L_DroMel_CAF1
Location 13,505,638 – 13,505,731
Length 93
Max. P 0.980083
window7443 window7444

overview

Window 3

Location 13,505,638 – 13,505,731
Length 93
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 87.16
Mean single sequence MFE -37.80
Consensus MFE -30.49
Energy contribution -31.27
Covariance contribution 0.78
Combinations/Pair 1.10
Mean z-score -4.00
Structure conservation index 0.81
SVM decision value 1.85
SVM RNA-class probability 0.980083
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13505638 93 + 22407834
AAACUGGAUUCCG------AGUGAGCUGCAGCAGAAGCUGCCGCUUCCUUGGCUUCCAGAUUCUCCAGAUCCGAUUUGCUGAGGAAAAUAAUGGAAUCC
...(((((..(((------((..(((.(((((....))))).)))..)))))..)))))....((((..(((..........)))......)))).... ( -36.70)
>DroPse_CAF1 152715 99 + 1
GUUCCGGCGUCCGCCAAGGAGGCAGCCGCUGCUGCAGCUGCCGCUUCCUUGGCCUCUAGAUUUUCCAAAUCGGUCUUGCUAAGGAAUAUAAUCGAGUCC
(((((((((.(((((((((((((.((.((((...)))).)).))))))))))).....((((.....))))))...))))..)))))............ ( -40.70)
>DroSec_CAF1 104414 93 + 1
AAACUGGAUUCCG------AGUGAGCUGCAGCAGAAGCUGCCGCUUCCUUGGCUUCCAGAUUCUCCAGAUCGGAUUUGCUGAGAAAAAUAAUGGAAUCC
...(((((..(((------((..(((.(((((....))))).)))..)))))..)))))....((((..((((.....)))).........)))).... ( -36.70)
>DroSim_CAF1 105960 93 + 1
AAACUGGAUUCCG------AGUGAGCUGCAGCAGAAGCUGCCGCUUCCUUGGCUUCCAGAUUCUCCAGAUCGGAUUUGCUGAGAAAAAUAAUGGAAUCC
...(((((..(((------((..(((.(((((....))))).)))..)))))..)))))....((((..((((.....)))).........)))).... ( -36.70)
>DroEre_CAF1 108907 93 + 1
AAACUGGAUUCCG------ACUGAGCUGCAGCGGACGCUGCUGCUUCCUUGGCUUCCAGAUUCUCCAGAUCGGUUUUGCUGAGGAAUAUAAUGGAAUCC
.....((((((((------....(((.(((((....))))).)))((((..((..((.((((.....))))))....))..))))......)))))))) ( -38.20)
>DroYak_CAF1 106828 93 + 1
AAACUGGAUUCCG------AUUGAGCUGCAGCAGAAGCUGCCGCUUCCUUGGCUUCCAGAUUCUCCAGAUCGGUUUUGCUGAGGAAAAUAAUGGAAUCC
.....((((((((------.....((.(((((....))))).))(((((..((..((.((((.....))))))....))..))))).....)))))))) ( -37.80)
>consensus
AAACUGGAUUCCG______AGUGAGCUGCAGCAGAAGCUGCCGCUUCCUUGGCUUCCAGAUUCUCCAGAUCGGAUUUGCUGAGGAAAAUAAUGGAAUCC
.....(((((((............((.(((((....))))).))(((((((((..((.((((.....))))))....)))))))))......))))))) (-30.49 = -31.27 +   0.78)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 13,505,638 – 13,505,731
Length 93
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 87.16
Mean single sequence MFE -34.83
Consensus MFE -28.80
Energy contribution -28.97
Covariance contribution 0.17
Combinations/Pair 1.12
Mean z-score -3.22
Structure conservation index 0.83
SVM decision value 1.56
SVM RNA-class probability 0.963771
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13505638 93 - 22407834
GGAUUCCAUUAUUUUCCUCAGCAAAUCGGAUCUGGAGAAUCUGGAAGCCAAGGAAGCGGCAGCUUCUGCUGCAGCUCACU------CGGAAUCCAGUUU
(((((((......(((((..((...(((((((....).))))))..))..)))))((.(((((....))))).)).....------.)))))))..... ( -35.60)
>DroPse_CAF1 152715 99 - 1
GGACUCGAUUAUAUUCCUUAGCAAGACCGAUUUGGAAAAUCUAGAGGCCAAGGAAGCGGCAGCUGCAGCAGCGGCUGCCUCCUUGGCGGACGCCGGAAC
((.(((((((...((((....(......)....))))))))..)))((((((((...(((((((((....))))))))))))))))).....))..... ( -40.20)
>DroSec_CAF1 104414 93 - 1
GGAUUCCAUUAUUUUUCUCAGCAAAUCCGAUCUGGAGAAUCUGGAAGCCAAGGAAGCGGCAGCUUCUGCUGCAGCUCACU------CGGAAUCCAGUUU
(((((((......((((.(((....(((.....)))....)))))))...((..(((.(((((....))))).)))..))------.)))))))..... ( -34.40)
>DroSim_CAF1 105960 93 - 1
GGAUUCCAUUAUUUUUCUCAGCAAAUCCGAUCUGGAGAAUCUGGAAGCCAAGGAAGCGGCAGCUUCUGCUGCAGCUCACU------CGGAAUCCAGUUU
(((((((......((((.(((....(((.....)))....)))))))...((..(((.(((((....))))).)))..))------.)))))))..... ( -34.40)
>DroEre_CAF1 108907 93 - 1
GGAUUCCAUUAUAUUCCUCAGCAAAACCGAUCUGGAGAAUCUGGAAGCCAAGGAAGCAGCAGCGUCCGCUGCAGCUCAGU------CGGAAUCCAGUUU
(((((((......(((((..((....((((((....).))).))..))..)))))((.(((((....))))).)).....------.)))))))..... ( -31.90)
>DroYak_CAF1 106828 93 - 1
GGAUUCCAUUAUUUUCCUCAGCAAAACCGAUCUGGAGAAUCUGGAAGCCAAGGAAGCGGCAGCUUCUGCUGCAGCUCAAU------CGGAAUCCAGUUU
(((((((......(((((..((....((((((....).))).))..))..)))))((.(((((....))))).)).....------.)))))))..... ( -32.50)
>consensus
GGAUUCCAUUAUUUUCCUCAGCAAAACCGAUCUGGAGAAUCUGGAAGCCAAGGAAGCGGCAGCUUCUGCUGCAGCUCACU______CGGAAUCCAGUUU
(((((((......(((((..((........(((((.....))))).))..)))))((.(((((....))))).))............)))))))..... (-28.80 = -28.97 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:08 2006