Locus 195

Sequence ID 2L_DroMel_CAF1
Location 588,466 – 588,592
Length 126
Max. P 0.999999
window290 window291 window292

overview

Window 0

Location 588,466 – 588,566
Length 100
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 79.21
Mean single sequence MFE -25.32
Consensus MFE -18.36
Energy contribution -17.43
Covariance contribution -0.94
Combinations/Pair 1.22
Mean z-score -1.69
Structure conservation index 0.73
SVM decision value 0.43
SVM RNA-class probability 0.733853
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 588466 100 + 22407834
CGUAAAAU----------AUAUGAUUAAAAGGAAAAAAAGCAACCCGCUUGUUUGUAUGCAUGCAUGUGUGUGUGACGUGCCAAUUUGCAUGGCGUUUCGUGCAUACAAA
.(((...(----------(((..(.(((..((............))..))).)..))))..))).((((((..(((..(((((.......)))))..)))..)))))).. ( -25.40)
>DroSec_CAF1 19773 100 + 1
CGUACAAU----------AUAUGAUUAAAAGGGGAAAAAACAACCCGCCUAUUUGUAUGUAUGUAUGUGUGAGUGACGCGCCAACUUGCAUGGCAUUUCGUACAUACAAA
........----------............(((..........))).....((((((((((((...((((.....))))((((.......))))....)))))))))))) ( -25.30)
>DroSim_CAF1 17568 99 + 1
CGUAAAAU----------AUAUGAUUAAAAUG-GAAAAAACAACCCGCCUAUUUGUAUGUAUGUGUGUGUGAGUGACGCGCCAACUUGCAUGGCAUUUCGUACAUACAAA
........----------..............-..................((((((((((((...((((.....))))((((.......))))....)))))))))))) ( -20.90)
>DroYak_CAF1 19927 110 + 1
CAUUAAAUCCUAUAAGAAAAAUGGUUUAAAGGGUGAAAAGCAACCCGCUUGCAUGUAUGUAUGUAUGUAAGGGCGACUUGCCAAUUUGCGUGGCACGUCGUACAUACAAA
..(((((.((............))))))).((((........)))).......((((((((((.((((.(((....)))((((.......)))))))))))))))))).. ( -29.70)
>consensus
CGUAAAAU__________AUAUGAUUAAAAGGGGAAAAAACAACCCGCCUAUUUGUAUGUAUGUAUGUGUGAGUGACGCGCCAACUUGCAUGGCAUUUCGUACAUACAAA
....................................................(((((((((((.....(((.....)))((((.......))))....))))))))))). (-18.36 = -17.43 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 1

Location 588,496 – 588,592
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 71.79
Mean single sequence MFE -31.43
Consensus MFE -23.28
Energy contribution -24.73
Covariance contribution 1.45
Combinations/Pair 1.13
Mean z-score -4.61
Structure conservation index 0.74
SVM decision value 6.08
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 588496 96 + 22407834
CAACCCGCUUGUUUGUAUGCAUGCAUGUGUGUGUGACGUGCCAAUUUGCAUGGCGUUUCGUGCAUACAAACAUACAUAAAUAUGUAUGUAAGUGCA
.....(((((..((((((((((((((....))))((..(((((.......)))))..))))))))))))((((((((....))))))))))))).. ( -33.10)
>DroSec_CAF1 19803 76 + 1
CAACCCGCCUAUUUGUAUGUAUGUAUGUGUGAGUGACGCGCCAACUUGCAUGGCAUUUCGUACAUACAAACAUACA--------------------
.............(((((((.((((((((((((.....)((((.......))))...))))))))))).)))))))-------------------- ( -23.10)
>DroYak_CAF1 19967 88 + 1
CAACCCGCUUGCAUGUAUGUAUGUAUGUAAGGGCGACUUGCCAAUUUGCGUGGCACGUCGUACAUACAAACAUACAUACAUAUU--------UGCA
......((..(.((((((((((((.((((.(..((((.(((((.......))))).))))..).)))).)))))))))))).).--------.)). ( -38.10)
>consensus
CAACCCGCUUGUUUGUAUGUAUGUAUGUGUGAGUGACGUGCCAAUUUGCAUGGCAUUUCGUACAUACAAACAUACAUA_AUAU_________UGCA
...............(((((((((.((((((..(((..(((((.......)))))..)))..)))))).))))))))).................. (-23.28 = -24.73 +   1.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 588,496 – 588,592
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 71.79
Mean single sequence MFE -28.50
Consensus MFE -20.82
Energy contribution -20.27
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -3.64
Structure conservation index 0.73
SVM decision value 6.79
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 588496 96 - 22407834
UGCACUUACAUACAUAUUUAUGUAUGUUUGUAUGCACGAAACGCCAUGCAAAUUGGCACGUCACACACACAUGCAUGCAUACAAACAAGCGGGUUG
.((...((((((......))))))((((((((((((......((((.......))))..((.....)).......)))))))))))).))...... ( -26.90)
>DroSec_CAF1 19803 76 - 1
--------------------UGUAUGUUUGUAUGUACGAAAUGCCAUGCAAGUUGGCGCGUCACUCACACAUACAUACAUACAAAUAGGCGGGUUG
--------------------(((((((.(((((((..((..(((((.......)))))..))......))))))).)))))))............. ( -22.30)
>DroYak_CAF1 19967 88 - 1
UGCA--------AAUAUGUAUGUAUGUUUGUAUGUACGACGUGCCACGCAAAUUGGCAAGUCGCCCUUACAUACAUACAUACAUGCAAGCGGGUUG
.((.--------..(((((((((((((.((((.(..((((.(((((.......))))).))))..).)))).)))))))))))))...))...... ( -36.30)
>consensus
UGCA_________AUAU_UAUGUAUGUUUGUAUGUACGAAAUGCCAUGCAAAUUGGCACGUCACACACACAUACAUACAUACAAACAAGCGGGUUG
....................(((.((((((((((((.(....((((.......))))..((.......))...).)))))))))))).)))..... (-20.82 = -20.27 +  -0.55)

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 09:28:57 2006