Locus 4550

Sequence ID 2L_DroMel_CAF1
Location 13,030,633 – 13,030,732
Length 99
Max. P 0.872812
window7171 window7172

overview

Window 1

Location 13,030,633 – 13,030,732
Length 99
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.41
Mean single sequence MFE -34.15
Consensus MFE -15.46
Energy contribution -15.80
Covariance contribution 0.34
Combinations/Pair 1.33
Mean z-score -2.00
Structure conservation index 0.45
SVM decision value -0.03
SVM RNA-class probability 0.520212
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13030633 99 + 22407834
UCUCCUCCUGCAGGAGCAGCUCUCGCUUCACUUGCUCCAGCGUGGGCACAUCCGGAACGGUAACUGUCAGGGAUUG---------------GCCACCCAUUACACCCACGCUCU
............((((((((....))......))))))((((((((...((((.((.(((...)))))..))))((---------------(....))).....)))))))).. ( -29.80)
>DroVir_CAF1 12257 99 + 1
UCUGCUUCUGCAGCUGCAGCUCACGCGCCACCUGCUCCAGCGUGGGCAUGUCCGGCACAGACAUGGUCAGCGACUG---------------GCCGCCCAUAACGCCGACGCUCU
...((.((.((.((((.(((.............))).))))(((((((((((.......)))))((((((...)))---------------)))))))))...)).)).))... ( -37.72)
>DroPse_CAF1 11657 114 + 1
UCUCCUCCUGCAGCUGCAGCUCUCGCUUCACCUGCUCCAAGGUGGGCACAUCCGGCACGGUCACCGUCAGGCCCUGUCCCACCACAUGGCUGCCCCCCAUCACGCCCACGCUCU
.........((((.((.(((....))).)).))))......((((((......(((((((...))))..((((.(((......))).))))))).........))))))..... ( -34.66)
>DroGri_CAF1 12714 99 + 1
UCUGCUCCUGCAGCUGCAGCUCACGCUUCACCUGCUCCAGCGUGGGCAUAUCCGGCACAGACAUGGCCAACGAUUG---------------GCCACCCAUCACGCCGACACUCU
.((((....)))).....(((((((((...........))))))))).....((((.......((((((.....))---------------))))........))))....... ( -34.36)
>DroAna_CAF1 4017 99 + 1
UCUCCUCCUGCCGCUGCAGCUCCCGCUUCACCUGCUCCAGUGUGGGUACAUCCGGCACCGUUACCGUGGGCGACUG---------------CCCGCCCAUCACACCCACACUCU
.........((.(.((.(((....))).)).).))...(((((((((.....(((........)))((((((....---------------..))))))....))))))))).. ( -33.70)
>DroPer_CAF1 11690 114 + 1
UCUCCUCCUGCAGCUGCAGCUCUCGCUUCACCUGCUCCAAGGUGGGCACAUCCGGCACGGUCACCGUCAGGCCCUGUCCCACCACAUGGCUGCCCCCCAUCACGCCCACGCUCU
.........((((.((.(((....))).)).))))......((((((......(((((((...))))..((((.(((......))).))))))).........))))))..... ( -34.66)
>consensus
UCUCCUCCUGCAGCUGCAGCUCUCGCUUCACCUGCUCCAGCGUGGGCACAUCCGGCACGGUCACCGUCAGCGACUG_______________GCCACCCAUCACGCCCACGCUCU
.........((((.((.(((....))).)).))))......((((((.....(((........))).(((...)))...........................))))))..... (-15.46 = -15.80 +   0.34)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,030,633 – 13,030,732
Length 99
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.41
Mean single sequence MFE -42.83
Consensus MFE -28.22
Energy contribution -28.62
Covariance contribution 0.39
Combinations/Pair 1.29
Mean z-score -1.66
Structure conservation index 0.66
SVM decision value 0.88
SVM RNA-class probability 0.872812
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13030633 99 - 22407834
AGAGCGUGGGUGUAAUGGGUGGC---------------CAAUCCCUGACAGUUACCGUUCCGGAUGUGCCCACGCUGGAGCAAGUGAAGCGAGAGCUGCUCCUGCAGGAGGAGA
..((((((((..((..(((....---------------....))).........(((...))).))..))))))))((((((......((....))))))))............ ( -36.80)
>DroVir_CAF1 12257 99 - 1
AGAGCGUCGGCGUUAUGGGCGGC---------------CAGUCGCUGACCAUGUCUGUGCCGGACAUGCCCACGCUGGAGCAGGUGGCGCGUGAGCUGCAGCUGCAGAAGCAGA
...((.(((((((...((((((.---------------(((...))).))(((((((...)))))))))))))))))).((((.((..((....))..)).))))....))... ( -42.90)
>DroPse_CAF1 11657 114 - 1
AGAGCGUGGGCGUGAUGGGGGGCAGCCAUGUGGUGGGACAGGGCCUGACGGUGACCGUGCCGGAUGUGCCCACCUUGGAGCAGGUGAAGCGAGAGCUGCAGCUGCAGGAGGAGA
...((((((((.(......).))..))))))(((((((((.(((...((((...)))))))...))).)))))).....((((.((.(((....))).)).))))......... ( -44.50)
>DroGri_CAF1 12714 99 - 1
AGAGUGUCGGCGUGAUGGGUGGC---------------CAAUCGUUGGCCAUGUCUGUGCCGGAUAUGCCCACGCUGGAGCAGGUGAAGCGUGAGCUGCAGCUGCAGGAGCAGA
...((.(((((((...(((((((---------------((.....)))))(((((((...)))))))))))))))))).((((.((.(((....))).)).))))....))... ( -44.30)
>DroAna_CAF1 4017 99 - 1
AGAGUGUGGGUGUGAUGGGCGGG---------------CAGUCGCCCACGGUAACGGUGCCGGAUGUACCCACACUGGAGCAGGUGAAGCGGGAGCUGCAGCGGCAGGAGGAGA
..((((((((((...(((((((.---------------...)))))))(((((....)))))....))))))))))...((.(.((.(((....))).)).).))......... ( -44.00)
>DroPer_CAF1 11690 114 - 1
AGAGCGUGGGCGUGAUGGGGGGCAGCCAUGUGGUGGGACAGGGCCUGACGGUGACCGUGCCGGAUGUGCCCACCUUGGAGCAGGUGAAGCGAGAGCUGCAGCUGCAGGAGGAGA
...((((((((.(......).))..))))))(((((((((.(((...((((...)))))))...))).)))))).....((((.((.(((....))).)).))))......... ( -44.50)
>consensus
AGAGCGUGGGCGUGAUGGGCGGC_______________CAGUCCCUGACGGUGACCGUGCCGGAUGUGCCCACGCUGGAGCAGGUGAAGCGAGAGCUGCAGCUGCAGGAGGAGA
..((((((((((((.(.((........................................)).).))))))))))))...((((.((.(((....))).)).))))......... (-28.22 = -28.62 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:49 2006