Locus 131

Sequence ID 3L_DroMel_CAF1
Location 415,238 – 415,363
Length 125
Max. P 0.999046
window184 window185 window186

overview

Window 4

Location 415,238 – 415,329
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 73.81
Mean single sequence MFE -29.35
Consensus MFE -17.60
Energy contribution -18.85
Covariance contribution 1.25
Combinations/Pair 1.27
Mean z-score -2.10
Structure conservation index 0.60
SVM decision value 1.66
SVM RNA-class probability 0.970470
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 415238 91 + 23771897
UGGCUUUCCUCACAUCACUUCACUAAACUGCUGCAGGUUCAGGGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAACAUCCC
......((((....(((((((.((.((((......)))).)))))))))..)))).((((((((((....))))))))))........... ( -28.30)
>DroGri_CAF1 73949 80 + 1
UCAGUUUAUUCACUUGGCUGCAC--AGCCUCAGCUGGUUGAGAGGGGUUUGUGGGUGGGAC----UGCGUGU-----CCUUUCCCCCUCCC
.........(((.(..((((...--.....))))..).)))((((((......((.(((((----.....))-----))).)))))))).. ( -26.50)
>DroSec_CAF1 62157 91 + 1
UGGCUUUCCUCACUUCACUUCACUAAACUGCGGCAGGUCCAGUGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAACCUCCU
.((...((((...((((((.((((..(((......)))..)))))))))).)))).((((((((((....)))))))))).....)).... ( -29.30)
>DroSim_CAF1 64292 91 + 1
UGGCUUUCCUCACUUCACUUCACUAAACUGCUGCAGGUCCAGGGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAGCCUCCU
.((((.((((...((((((((.((..(((......)))..)))))))))).)))).((((((((((....))))))))))...)))).... ( -33.30)
>consensus
UGGCUUUCCUCACUUCACUUCACUAAACUGCUGCAGGUCCAGGGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAACCUCCC
........(((...(((((((.((.((((......)))).)))))))))...))).((((((((((....))))))))))........... (-17.60 = -18.85 +   1.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 415,256 – 415,363
Length 107
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 72.63
Mean single sequence MFE -39.15
Consensus MFE -19.81
Energy contribution -22.25
Covariance contribution 2.44
Combinations/Pair 1.40
Mean z-score -4.27
Structure conservation index 0.51
SVM decision value 3.34
SVM RNA-class probability 0.999046
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 415256 107 + 23771897
UUCACUAAACUGCUGCAGGUUCAGGGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAACAUCCCCAUUCCACCCCC---UUGUGCUGUGGUCAGUU-UAAUC
.....((((((((..(((....((((((((.((.(((.((((((((((....)))))))))).........))).)).)))))))---)....)))..).)))))-))... ( -48.20)
>DroGri_CAF1 73967 100 + 1
UGCAC--AGCCUCAGCUGGUUGAGAGGGGUUUGUGGGUGGGAC----UGCGUGU-----CCUUUCCCCCUCCCAAUGCCAGCCCCCUUUUUUCCUGUGGUCAGCUGUAAUC
...((--(((....((.((..((((((((.(((((((.(((((----.....))-----)))........))))....))).))))))))..)).)).....))))).... ( -36.00)
>DroSec_CAF1 62175 107 + 1
UUCACUAAACUGCGGCAGGUCCAGUGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAACCUCCUCUUUCCACCCCC---UCGUGCUGUGGUCAGUU-UAAUC
.....((((((((.((((..(.((.(((((.((((((.((((((((((....)))))))))).........)))))).))))).)---).)..)))).).)))))-))... ( -42.10)
>DroSim_CAF1 64310 107 + 1
UUCACUAAACUGCUGCAGGUCCAGGGGGUGAAAAGGGUGGCUAUAUACACGUGUAUAUGGCCUUCAGCCUCCUCUUUCCACCCCC---UCGUGCUGUGGUCAGUU-UAAUC
.....((((((((..(((..(.((((((((.((((((.((((((((((....)))))))))).........)))))).)))))))---).)..)))..).)))))-))... ( -50.10)
>DroEre_CAF1 66427 82 + 1
UUCACUAAACUGCUGCAGGUCCAG-GGGUGAAAGG------------------------GCCUUCAACCUCCUCUUUCCACCCCC---UCGUGCUGCGGUCAGUU-UAAUC
.....(((((((((((((.....(-((((((((((------------------------(...........)))))).)))))).---.....)))))).)))))-))... ( -31.90)
>DroYak_CAF1 66602 81 + 1
UUCACUAAACUGCUGCAGGUCC-G-GGGUGAAAAG------------------------GCCUUCAACCUCCUCUUUCCACCCCC---UCGUGCUGUGGUCAGUU-UAAUC
.....((((((((..(((....-(-(((((.((((------------------------(............))))).)))))).---.....)))..).)))))-))... ( -26.60)
>consensus
UUCACUAAACUGCUGCAGGUCCAG_GGGUGAAAAGGGUGGCUA____CACGUGU_____GCCUUCAACCUCCUCUUUCCACCCCC___UCGUGCUGUGGUCAGUU_UAAUC
........(((((.(((.(......(((((.((((((.((((((((((....)))))))))).........)))))).)))))......).))).)))))........... (-19.81 = -22.25 +   2.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 415,256 – 415,363
Length 107
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 72.63
Mean single sequence MFE -39.27
Consensus MFE -11.66
Energy contribution -13.58
Covariance contribution 1.92
Combinations/Pair 1.12
Mean z-score -3.88
Structure conservation index 0.30
SVM decision value 3.00
SVM RNA-class probability 0.998064
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 415256 107 - 23771897
GAUUA-AACUGACCACAGCACAA---GGGGGUGGAAUGGGGAUGUUGAAGGCCAUAUACACGUGUAUAUAGCCACCCUUUUCACCCCCUGAACCUGCAGCAGUUUAGUGAA
.((((-(((((.(..(((....(---((((((((((.(((.........(((.((((((....)))))).))).))).)))))))))))....)))..))))))))))... ( -46.20)
>DroGri_CAF1 73967 100 - 1
GAUUACAGCUGACCACAGGAAAAAAGGGGGCUGGCAUUGGGAGGGGGAAAGG-----ACACGCA----GUCCCACCCACAAACCCCUCUCAACCAGCUGAGGCU--GUGCA
...(((((((..((...........)).((((((..((((((((((....((-----((.....----))))..........))))))))))))))))..))))--))).. ( -39.34)
>DroSec_CAF1 62175 107 - 1
GAUUA-AACUGACCACAGCACGA---GGGGGUGGAAAGAGGAGGUUGAAGGCCAUAUACACGUGUAUAUAGCCACCCUUUUCACCCACUGGACCUGCCGCAGUUUAGUGAA
.((((-(((((....(((..(.(---(.((((((((((....(((....(((.((((((....)))))).)))))))))))))))).)).)..)))...)))))))))... ( -39.80)
>DroSim_CAF1 64310 107 - 1
GAUUA-AACUGACCACAGCACGA---GGGGGUGGAAAGAGGAGGCUGAAGGCCAUAUACACGUGUAUAUAGCCACCCUUUUCACCCCCUGGACCUGCAGCAGUUUAGUGAA
.((((-(((((.(..(((..(.(---((((((((((((.((.((((.......((((((....)))))))))).))))))))))))))).)..)))..))))))))))... ( -49.21)
>DroEre_CAF1 66427 82 - 1
GAUUA-AACUGACCGCAGCACGA---GGGGGUGGAAAGAGGAGGUUGAAGGC------------------------CCUUUCACCC-CUGGACCUGCAGCAGUUUAGUGAA
.((((-(((((.(.((((..(.(---((((...(((((.((..........)------------------------)))))).)))-)).)..)))).))))))))))... ( -33.50)
>DroYak_CAF1 66602 81 - 1
GAUUA-AACUGACCACAGCACGA---GGGGGUGGAAAGAGGAGGUUGAAGGC------------------------CUUUUCACCC-C-GGACCUGCAGCAGUUUAGUGAA
.((((-(((((.(..(((.....---((((.(....)((((((((.....))------------------------)))))).)))-)-....)))..))))))))))... ( -27.60)
>consensus
GAUUA_AACUGACCACAGCACGA___GGGGGUGGAAAGAGGAGGUUGAAGGC_____ACACGUG____UAGCCACCCUUUUCACCC_CUGGACCUGCAGCAGUUUAGUGAA
.((((.(((((......(((......((((((((((((......................................)))))))))).)).....)))..)))))))))... (-11.66 = -13.58 +   1.92)

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 09:33:25 2006