Locus 5332

Sequence ID X_DroMel_CAF1
Location 13,922,014 – 13,922,199
Length 185
Max. P 0.755743
window8636 window8637 window8638

overview

Window 6

Location 13,922,014 – 13,922,124
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.84
Mean single sequence MFE -36.64
Consensus MFE -12.16
Energy contribution -12.96
Covariance contribution 0.80
Combinations/Pair 1.15
Mean z-score -1.90
Structure conservation index 0.33
SVM decision value 0.49
SVM RNA-class probability 0.755743
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13922014 110 + 22224390
AAA-AUGGUGGACUGGAAAGGAGGG-----GGUGGGGGUGGUGGGCGGGUUUUUGCGGAAAGAAUGUCAGUGUCUUUCAAGGAUUCGUCGUUGGCCCC----ACGCUCCCAGGAUCCGCC
...-..((((((((....))..(((-----(((((((((.(..(((((((((((...((((((.........)))))))))))))))))..).)))))----.)))))))....)))))) ( -48.40)
>DroSec_CAF1 2230 89 + 1
-AA-AUGGUGGGUUGGGAACGUUGG-----GG--------------------CUGCGGAAAGAAUGUCAGUGUCUUUCAAGGAUUCGUCGUUGGCCCC----CUGCUCCCAGGAUCCGCC
-..-..((((((((((((.((..((-----((--------------------((((((...((..(((..((.....))..))))).))).)))))))----.)).)))))..))))))) ( -35.10)
>DroSim_CAF1 4227 89 + 1
-AA-AUGGUGGCUUGGAAACGUGGG-----GG--------------------CUGCGGAAAGAAUGUCAGUGUCUUUCAAGGAUUCGUCGUUGGCCCC----CUGCUCCCAGGAUCCGCC
-..-..((((((((((...((.(((-----((--------------------((((((...((..(((..((.....))..))))).))).)))))))----)))...)))))..))))) ( -33.90)
>DroEre_CAF1 3726 94 + 1
-AAAAGGGAGGGGUGAAAACAGGGGCAGGCGG--------------------UUGUGGAAAGAACGUCAGUGUCUUUCAAGGAUUCGUCGUUGGCCC-----CCACUCCCAGGCUCCACC
-....(((((..((....)).(((((.(((((--------------------((.(.((((((((....)).)))))).).)).)))))....))))-----)..))))).......... ( -35.30)
>DroYak_CAF1 3712 91 + 1
-AA-AUGGUGGGGUGCAAAGGGG-------GG--------------------UUGUGGAAAGAAUGUCAGUGUCUUUCAAGGAUUCGUCUUUGGCCCCAAACCCGCUGCCAGGAACCUCC
-..-..((((((((.((((((.(-------((--------------------((.(.((((((.........)))))).).))))).)))))))))))....((.......)).)))... ( -30.50)
>consensus
_AA_AUGGUGGGGUGGAAACGGGGG_____GG____________________UUGCGGAAAGAAUGUCAGUGUCUUUCAAGGAUUCGUCGUUGGCCCC____CCGCUCCCAGGAUCCGCC
......((((((((...........................................((((((((....)).))))))............((((..............)))))))))))) (-12.16 = -12.96 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,922,088 – 13,922,199
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.23
Mean single sequence MFE -38.86
Consensus MFE -28.06
Energy contribution -28.86
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.72
SVM decision value 0.16
SVM RNA-class probability 0.613241
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13922088 111 + 22224390
GGAUUCGUCGUUGGCCCC----ACGCUCCCAGGAUCCGCCACUUCCAUCCGGGGAAUAUCU-----CCCCCUUUUUCUGCUUUUGACUUUGGCGUGACAAAUGCAUGGGGCCAAUGGGCA
......((((((((((((----(.((((....))(((((((.........(((((.....)-----)))).....((.......))...))))).)).....)).)))))))))).))). ( -41.50)
>DroSec_CAF1 2283 111 + 1
GGAUUCGUCGUUGGCCCC----CUGCUCCCAGGAUCCGCCACUUCCAUCCGGGGAAUAUCU-----CCCCCUUUUUCUGCUUUUGACUUUGGCGUGACAAAUGCAUGGGGCCAAUGGGCA
......((((((((((((----.(((((....))(((((((.........(((((.....)-----)))).....((.......))...))))).)).....))).))))))))).))). ( -41.50)
>DroSim_CAF1 4280 111 + 1
GGAUUCGUCGUUGGCCCC----CUGCUCCCAGGAUCCGCCACUUCCAUCCGGGGAAUAUCU-----CCCCCUUUUUCUGCUUUUGACUUUGGCGUGACAAAUGCAUGGGGCCAAUGGGCA
......((((((((((((----.(((((....))(((((((.........(((((.....)-----)))).....((.......))...))))).)).....))).))))))))).))). ( -41.50)
>DroEre_CAF1 3785 110 + 1
GGAUUCGUCGUUGGCCC-----CCACUCCCAGGCUCCACCACUUUCAUCCGGGGAAUAUGU-----CCCCCUUUUUCAGCUUCUGACUUUGGCGUGACAAAUGCAUGGGACCAAUGGGCA
.............((((-----....(((((.((.....(((........(((((.....)-----))))........(((.........))))))......)).))))).....)))). ( -30.20)
>DroYak_CAF1 3763 120 + 1
GGAUUCGUCUUUGGCCCCAAACCCGCUGCCAGGAACCUCCACUUUCAACCGGGGAAUAUAUAUCUCCCCCCUUUUUCUGCUGCUGACUUUGGCGUGACAAAUGCAUGGGGCCAAUGGGCA
......(((((((((((((.....((.((..((.....))..........(((((.........))))).........)).))........((((.....)))).))))))))).)))). ( -39.60)
>consensus
GGAUUCGUCGUUGGCCCC____CCGCUCCCAGGAUCCGCCACUUCCAUCCGGGGAAUAUCU_____CCCCCUUUUUCUGCUUUUGACUUUGGCGUGACAAAUGCAUGGGGCCAAUGGGCA
......((((((((((((......((.....((.....))..........((((.............)))).......))...........((((.....))))..))))))))).))). (-28.06 = -28.86 +   0.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,922,088 – 13,922,199
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.23
Mean single sequence MFE -42.72
Consensus MFE -29.34
Energy contribution -29.02
Covariance contribution -0.32
Combinations/Pair 1.21
Mean z-score -2.24
Structure conservation index 0.69
SVM decision value 0.06
SVM RNA-class probability 0.561851
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13922088 111 - 22224390
UGCCCAUUGGCCCCAUGCAUUUGUCACGCCAAAGUCAAAAGCAGAAAAAGGGGG-----AGAUAUUCCCCGGAUGGAAGUGGCGGAUCCUGGGAGCGU----GGGGCCAACGACGAAUCC
......((((((((((((.((((((((.(((..((.....)).......(((((-----(....))))))...)))..))))))))((....))))))----)))))))).......... ( -46.50)
>DroSec_CAF1 2283 111 - 1
UGCCCAUUGGCCCCAUGCAUUUGUCACGCCAAAGUCAAAAGCAGAAAAAGGGGG-----AGAUAUUCCCCGGAUGGAAGUGGCGGAUCCUGGGAGCAG----GGGGCCAACGACGAAUCC
......((((((((.(((.((((((((.(((..((.....)).......(((((-----(....))))))...)))..))))))))((....))))).----)))))))).......... ( -42.60)
>DroSim_CAF1 4280 111 - 1
UGCCCAUUGGCCCCAUGCAUUUGUCACGCCAAAGUCAAAAGCAGAAAAAGGGGG-----AGAUAUUCCCCGGAUGGAAGUGGCGGAUCCUGGGAGCAG----GGGGCCAACGACGAAUCC
......((((((((.(((.((((((((.(((..((.....)).......(((((-----(....))))))...)))..))))))))((....))))).----)))))))).......... ( -42.60)
>DroEre_CAF1 3785 110 - 1
UGCCCAUUGGUCCCAUGCAUUUGUCACGCCAAAGUCAGAAGCUGAAAAAGGGGG-----ACAUAUUCCCCGGAUGAAAGUGGUGGAGCCUGGGAGUGG-----GGGCCAACGACGAAUCC
.((((.(((.(((((.((.((..((((.((....((((...))))....(((((-----(....))))))))......))))..)))).))))).)))-----))))............. ( -39.70)
>DroYak_CAF1 3763 120 - 1
UGCCCAUUGGCCCCAUGCAUUUGUCACGCCAAAGUCAGCAGCAGAAAAAGGGGGGAGAUAUAUAUUCCCCGGUUGAAAGUGGAGGUUCCUGGCAGCGGGUUUGGGGCCAAAGACGAAUCC
......(((((((((.((..(((((...(((...(((((..(.......)((((((........)))))).)))))...)))((....)))))))...)).))))))))).......... ( -42.20)
>consensus
UGCCCAUUGGCCCCAUGCAUUUGUCACGCCAAAGUCAAAAGCAGAAAAAGGGGG_____AGAUAUUCCCCGGAUGGAAGUGGCGGAUCCUGGGAGCGG____GGGGCCAACGACGAAUCC
......((((((((............(((((...(((............(((((...........)))))...)))...)))))....(((....)))....)))))))).......... (-29.34 = -29.02 +  -0.32)

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 11:45:13 2006