Locus 5060

Sequence ID 2L_DroMel_CAF1
Location 14,490,767 – 14,490,907
Length 140
Max. P 0.987655
window8046 window8047 window8048

overview

Window 6

Location 14,490,767 – 14,490,869
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 94.31
Mean single sequence MFE -46.56
Consensus MFE -39.34
Energy contribution -40.02
Covariance contribution 0.68
Combinations/Pair 1.08
Mean z-score -2.12
Structure conservation index 0.84
SVM decision value 2.09
SVM RNA-class probability 0.987655
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14490767 102 + 22407834
GUGUGCAGCGCUGCUCGCCGGAGAGCGCUCUCUCGCGAGUGAGCGAACGCUUCGCUGCGAGGGCAGUUACGCUCGCUGCCGCAGUCGUUGAAUUCAAUUCGA
(((.(((((...((((((.(((((....))))).))))))((((((((.(((((...)))))...))).)))))))))))))....((((....)))).... ( -44.90)
>DroSec_CAF1 22492 102 + 1
GUGUGCAGCGCUGCUCGCCGGAGAGCGCUCUCUCGCAAGUGAGCGAACGCUUCGCUGCGAGGGCAGCUACGCUCGCGGCCGCAGUCGUUGAAUUCAAUUCGA
.((..(((((((((..((((..(((((((((((((((.((((((....)).)))))))))))).)))...)))).)))).)))).)))))....))...... ( -50.10)
>DroSim_CAF1 6536 102 + 1
GUGUGCAGCGCUGCUCGCCGGAGAGCGCUCUCUCGCAAGUGAGCGAACGCUUCGCUGCGAGGGCAGUUACGCUCGCGGCCGCAGUCGUUGAAUUCAAUUCGA
.((..(((((((((..((((..(((((((((((((((.((((((....)).)))))))))))).))...))))).)))).)))).)))))....))...... ( -49.10)
>DroEre_CAF1 16412 102 + 1
GUGUGCAGCGCUGCUCGCCGGAGAGAGCUCUCUCGCGUGAGAACGAACGCUUCGCUGCGAGGGCAGCUACACUCGCGGCCGCUGUCGUUGAAUUCAAUUCGA
.((..((((((.((..(((((((.(((((((((((((((((.........))))).))))))).)))).).))).)))).)).).)))))....))...... ( -40.70)
>DroYak_CAF1 11651 102 + 1
GUGUGCAGCGCUGCUCGCCGGAGAGAGCGCUCUCGCGUGAGAACGAACGCUUCGCUGCGAGGGCAGUUACACUCGCGGCGGCAGUCGUUGAAUUCAAUUCGA
.((..(((((((((.((((((((.(((((((((((((((((.........))))).)))))))).))).).))).))))))))).)))))....))...... ( -48.00)
>consensus
GUGUGCAGCGCUGCUCGCCGGAGAGCGCUCUCUCGCGAGUGAGCGAACGCUUCGCUGCGAGGGCAGUUACGCUCGCGGCCGCAGUCGUUGAAUUCAAUUCGA
.((..(((((((((..((((..(((((((((((((((.((((((....).))))))))))))).)))...)))).)))).)))).)))))....))...... (-39.34 = -40.02 +   0.68)

alignment

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secondary structure

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Window 7

Location 14,490,767 – 14,490,869
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 94.31
Mean single sequence MFE -39.90
Consensus MFE -37.56
Energy contribution -37.08
Covariance contribution -0.48
Combinations/Pair 1.06
Mean z-score -1.32
Structure conservation index 0.94
SVM decision value 1.03
SVM RNA-class probability 0.903444
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14490767 102 - 22407834
UCGAAUUGAAUUCAACGACUGCGGCAGCGAGCGUAACUGCCCUCGCAGCGAAGCGUUCGCUCACUCGCGAGAGAGCGCUCUCCGGCGAGCAGCGCUGCACAC
(((..(((....)))))).(((((((((((((((..((((....))))....)))))))))..((((((((((....)))))..)))))....))))))... ( -41.40)
>DroSec_CAF1 22492 102 - 1
UCGAAUUGAAUUCAACGACUGCGGCCGCGAGCGUAGCUGCCCUCGCAGCGAAGCGUUCGCUCACUUGCGAGAGAGCGCUCUCCGGCGAGCAGCGCUGCACAC
(((..(((....)))))).((((((.((((((((.(((((....)))))...))))))((((.((.(.(((((....)))))))).)))).))))))))... ( -43.40)
>DroSim_CAF1 6536 102 - 1
UCGAAUUGAAUUCAACGACUGCGGCCGCGAGCGUAACUGCCCUCGCAGCGAAGCGUUCGCUCACUUGCGAGAGAGCGCUCUCCGGCGAGCAGCGCUGCACAC
............((.((.((((.((((((((.((....)).))))).(.(((((((((.(((......))).))))))).))))))..)))))).))..... ( -38.60)
>DroEre_CAF1 16412 102 - 1
UCGAAUUGAAUUCAACGACAGCGGCCGCGAGUGUAGCUGCCCUCGCAGCGAAGCGUUCGUUCUCACGCGAGAGAGCUCUCUCCGGCGAGCAGCGCUGCACAC
(((..(((....))))))..(((((.((((((((.(((((....)))))...))))))((((.(.((.(((((....)))))))).)))).))))))).... ( -38.50)
>DroYak_CAF1 11651 102 - 1
UCGAAUUGAAUUCAACGACUGCCGCCGCGAGUGUAACUGCCCUCGCAGCGAAGCGUUCGUUCUCACGCGAGAGCGCUCUCUCCGGCGAGCAGCGCUGCACAC
(((..(((....)))))).((((((.(((((.((....)).))))).))).((((((.((((((....))))))((((.(....).)))))))))))))... ( -37.60)
>consensus
UCGAAUUGAAUUCAACGACUGCGGCCGCGAGCGUAACUGCCCUCGCAGCGAAGCGUUCGCUCACUCGCGAGAGAGCGCUCUCCGGCGAGCAGCGCUGCACAC
(((..(((....))))))..((.((.(((((.((....)).))))).))..((((((.((((.(.((.(((((....)))))))).)))))))))))).... (-37.56 = -37.08 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,490,803 – 14,490,907
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.67
Mean single sequence MFE -37.68
Consensus MFE -26.18
Energy contribution -26.10
Covariance contribution -0.08
Combinations/Pair 1.23
Mean z-score -1.58
Structure conservation index 0.69
SVM decision value 0.04
SVM RNA-class probability 0.551555
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14490803 104 + 22407834
GAGUGAG------CGAACG--------CUUCGCUGCGAGGGCAGUUACGCUCGCUGCCGCAGUCGUUGAAUUCAAUUCGAAUUUUGACUUCGCAGCGUUCAGACGU-GUUCGGAAA-AAC
.......------((((((--------(..((((((((.((((((.......))))))..(((((..((((((.....))))))))))))))))))).......))-)))))....-... ( -39.20)
>DroSec_CAF1 22528 104 + 1
AAGUGAG------CGAACG--------CUUCGCUGCGAGGGCAGCUACGCUCGCGGCCGCAGUCGUUGAAUUCAAUUCGAAUUUUGACUUCGCAGCGUUCAGACGU-GUUCGGAAA-AAC
.......------((((((--------(.(((((((....))))).(((((.((((....(((((..((((((.....))))))))))))))))))))...)).))-)))))....-... ( -38.10)
>DroSim_CAF1 6572 104 + 1
AAGUGAG------CGAACG--------CUUCGCUGCGAGGGCAGUUACGCUCGCGGCCGCAGUCGUUGAAUUCAAUUCGAAUUUUGACUUCGCAGCGUUCAGACGU-GUUCGGAAA-AAC
.......------((((((--------(.((((((((((.(......).))))))))((((((((..((((((.....))))))))))).....)))....)).))-)))))....-... ( -36.60)
>DroEre_CAF1 16448 103 + 1
GUGAGAA------CGAACG--------CUUCGCUGCGAGGGCAGCUACACUCGCGGCCGCUGUCGUUGAAUUCAAUUCGAGUUUAGACUUCGCAGCGUUCAGACGU-GUUCGGAA--AAC
.......------((((((--------(.(((((((((((.......).))))))))((((((..((((((((.....)))))))).....))))))....)).))-)))))...--... ( -40.00)
>DroYak_CAF1 11687 103 + 1
GUGAGAA------CGAACG--------CUUCGCUGCGAGGGCAGUUACACUCGCGGCGGCAGUCGUUGAAUUCAAUUCGAGUUUAGACUUCGCAGCGUUCAGACGU-GUUCGGAA--AAC
.......------((((((--------(..((((((((((....(((.(((((((((....))))).((((...)))))))).))).)))))))))).......))-)))))...--... ( -38.10)
>DroPer_CAF1 5708 120 + 1
GAGUGAGCGUGCACGAACGUGUCCGUUCUUCACUUUGCGGCUAGGUACGUUCGCACCGUCACACGGAGAAUACAGUUCGAGUUCAGCCUUCGAAUCGUUCAGACGUUGCUCGGAAAAAAG
..((((((((((..(((((....)))))....((........)))))))))))).(((.((.(((..((((...(((((((.......))))))).))))...)))))..)))....... ( -34.10)
>consensus
GAGUGAG______CGAACG________CUUCGCUGCGAGGGCAGUUACGCUCGCGGCCGCAGUCGUUGAAUUCAAUUCGAAUUUAGACUUCGCAGCGUUCAGACGU_GUUCGGAAA_AAC
.............(((((............((((((((((((.((..(....)..)).)).......((((((.....))))))...))))))))))..........)))))........ (-26.18 = -26.10 +  -0.08)

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 11:34:52 2006