Locus 543

Sequence ID 3R_DroMel_CAF1
Location 2,031,148 – 2,031,267
Length 119
Max. P 0.977884
window864 window865

overview

Window 4

Location 2,031,148 – 2,031,267
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.49
Mean single sequence MFE -32.62
Consensus MFE -19.69
Energy contribution -20.67
Covariance contribution 0.97
Combinations/Pair 1.20
Mean z-score -2.34
Structure conservation index 0.60
SVM decision value 1.80
SVM RNA-class probability 0.977884
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2031148 119 + 27905053
UCGCUUGGUAUUUGCUUCUUGUUAACUUAAUUAACAACAUACCAUUU-UCCACUACAGGUUUGAAGAAGGUGAUGUGGCCCAUCUAUAUGGGUUUGCAAGUGCUGAAGAGCGUGCUCUUC
......(((((((((....((((((.....))))))(((((((.(((-((.((.....))..))))).))).))))(((((((....))))))).)))))))))((((((....)))))) ( -35.10)
>DroSec_CAF1 174163 117 + 1
UCGCUUUGUACUUGCAUCUUGUA---UUAAAUAACUAUAUACCAUUUUUCUACUCCAGGUUUGAAGAAGGUGAUGUGGCCCAUCUACAUGGGUCUGCAAGUGCUGAAGAGCGUGCUCUUC
.......(((((((((.......---.............((((.((((((.((.....))..))))))))))....(((((((....)))))))))))))))).((((((....)))))) ( -37.20)
>DroSim_CAF1 179101 117 + 1
UCGCUUUGUACUUGCAUCUUGUA---UAAAAUAACUAUAUACCAUUUUUCUACUCCAGGUUUGAAGAAGGUGAUGUGGCCCAUCUACAUGGGUCUGCAAGUGCUGAAGAGCGUGCUCUUC
.......(((((((((.......---.............((((.((((((.((.....))..))))))))))....(((((((....)))))))))))))))).((((((....)))))) ( -37.20)
>DroEre_CAF1 174785 100 + 1
ACACUUGGUA--------------------CUAACCACAUCCCAUUUUUCCACUCCAGGCUUGAAGAAGGUGAUGUGGCCCAUCUACAUGGGUCUGCAAGUGCUGAAGAGCGUGCUCUUC
.((((((...--------------------....(((((((((.(((((((......))...))))).)).)))))))(((((....)))))....))))))..((((((....)))))) ( -34.60)
>DroYak_CAF1 177439 117 + 1
ACACUUGGUACAUUGUUCUUGUA---UUAACUAACGACAUACCAAUUUUCCACACCAGGUUUGAAGAAGGUGAUGUGGCCCAUAUACAUGGGACUGCAAGUGCUGAAGAGCGUGCUCUUC
.(((((((((..(((((...((.---...)).)))))..)))))........((((............)))).((..((((((....))))).)..))))))..((((((....)))))) ( -31.40)
>DroPer_CAF1 153813 92 + 1
--------------------------UUACAC-AAAACAUACGAUU-UUCCAUUGCAGGCUUGAAGAAAAUAAUGUGGCCCAUAUAUAUGGGAUUACAGGUGCUGAAGAGUGUGCUUUUU
--------------------------......-.............-.......(((.((((..((.......((((((((((....))))).)))))....))...)))).)))..... ( -20.20)
>consensus
UCGCUUGGUACUUGC_UCUUGUA___UUAAAUAACAACAUACCAUUUUUCCACUCCAGGUUUGAAGAAGGUGAUGUGGCCCAUCUACAUGGGUCUGCAAGUGCUGAAGAGCGUGCUCUUC
.......((((............................((((.((((((............)))))))))).((((((((((....))))).))))).)))).((((((....)))))) (-19.69 = -20.67 +   0.97)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,031,148 – 2,031,267
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.49
Mean single sequence MFE -29.39
Consensus MFE -14.83
Energy contribution -15.50
Covariance contribution 0.67
Combinations/Pair 1.13
Mean z-score -2.03
Structure conservation index 0.50
SVM decision value 0.68
SVM RNA-class probability 0.820552
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2031148 119 - 27905053
GAAGAGCACGCUCUUCAGCACUUGCAAACCCAUAUAGAUGGGCCACAUCACCUUCUUCAAACCUGUAGUGGA-AAAUGGUAUGUUGUUAAUUAAGUUAACAAGAAGCAAAUACCAAGCGA
((((((....)))))).....((((...(((((....)))))((((.....................)))).-...((((((.((((((((...)))))))).......)))))).)))) ( -28.30)
>DroSec_CAF1 174163 117 - 1
GAAGAGCACGCUCUUCAGCACUUGCAGACCCAUGUAGAUGGGCCACAUCACCUUCUUCAAACCUGGAGUAGAAAAAUGGUAUAUAGUUAUUUAA---UACAAGAUGCAAGUACAAAGCGA
((((((....)))))).(.((((((.(.(((((....))))).)..(((..((.(((((....))))).)).......((((.(((....))))---)))..))))))))).)....... ( -29.80)
>DroSim_CAF1 179101 117 - 1
GAAGAGCACGCUCUUCAGCACUUGCAGACCCAUGUAGAUGGGCCACAUCACCUUCUUCAAACCUGGAGUAGAAAAAUGGUAUAUAGUUAUUUUA---UACAAGAUGCAAGUACAAAGCGA
((((((....)))))).(.((((((.(.(((((....))))).)..(((..((.(((((....))))).)).......(((((.........))---)))..))))))))).)....... ( -31.30)
>DroEre_CAF1 174785 100 - 1
GAAGAGCACGCUCUUCAGCACUUGCAGACCCAUGUAGAUGGGCCACAUCACCUUCUUCAAGCCUGGAGUGGAAAAAUGGGAUGUGGUUAG--------------------UACCAAGUGU
((((((....)))))).(((((((....(((((....)))))(((((((.((..(((((....))))).........)))))))))....--------------------...))))))) ( -36.50)
>DroYak_CAF1 177439 117 - 1
GAAGAGCACGCUCUUCAGCACUUGCAGUCCCAUGUAUAUGGGCCACAUCACCUUCUUCAAACCUGGUGUGGAAAAUUGGUAUGUCGUUAGUUAA---UACAAGAACAAUGUACCAAGUGU
((((((....)))))).((((((.....(((((....)))))((((((((.............))))))))......(((((((.(((.((...---.))...))).))))))))))))) ( -35.92)
>DroPer_CAF1 153813 92 - 1
AAAAAGCACACUCUUCAGCACCUGUAAUCCCAUAUAUAUGGGCCACAUUAUUUUCUUCAAGCCUGCAAUGGAA-AAUCGUAUGUUUU-GUGUAA--------------------------
.....(((((..................(((((....)))))..((((.(((((((....(....)...))))-)))...))))..)-))))..-------------------------- ( -14.50)
>consensus
GAAGAGCACGCUCUUCAGCACUUGCAGACCCAUGUAGAUGGGCCACAUCACCUUCUUCAAACCUGGAGUGGAAAAAUGGUAUGUAGUUAUUUAA___UACAAGA_GCAAGUACCAAGCGA
((((((....)))))).((....))...(((((....)))))(((......((.(((((....))))).)).....)))......................................... (-14.83 = -15.50 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:38 2006