Locus 6314

Sequence ID 2L_DroMel_CAF1
Location 17,599,121 – 17,599,366
Length 245
Max. P 0.679899
window10091 window10092 window10093

overview

Window 1

Location 17,599,121 – 17,599,224
Length 103
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 73.33
Mean single sequence MFE -25.63
Consensus MFE -15.12
Energy contribution -16.29
Covariance contribution 1.17
Combinations/Pair 1.35
Mean z-score -1.42
Structure conservation index 0.59
SVM decision value 0.30
SVM RNA-class probability 0.679899
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17599121 103 + 22407834
GAAGUUUUUCGUGCCAAAAAUGCUACGGCUCAAUGGGUUCCACUGCAAGAACCGGCAAACAAUUUGGCCA------CAUCGGCCAAAAGUUCAAA--------GAACUAGAGUUUUG
..(((((((..((((......((....))......(((((........))))))))).....(((((((.------....)))))))......))--------)))))......... ( -30.10)
>DroVir_CAF1 2509 106 + 1
GAAAUGUUUCGGGCCAAGAACGCAACAGCUCAGUGGGUAUCGCUGCAGGAGCCGGCCAACAACUUGAGUG------CCACAGCCAAGACAACAA--CCAA---AAAUUAGAAUCCAC
((..((((.((..(...)..)).))))..)).((((((.(((((((....).))))......((((.((.------.....)))))).......--....---......)))))))) ( -20.50)
>DroEre_CAF1 2665 103 + 1
GAAGUUUUUCGUGCCAAAAAUGCCACGGCUCAAUGGGUUCCACUGCAAGAACCUGCAAACAAUUUGGCCA------CAGCAGCCAAAAGUUCAAA--------GAACUAGAGUCCUC
..........(((.((....)).)))(((((...((((((........))))))........((((((..------.....))))))(((((...--------))))).)))))... ( -24.60)
>DroWil_CAF1 1371 109 + 1
GAAAUGUUUCGGGCCAAAAAUGCUACUGCACAAUGGGUGCCAUUGCAAGAGCCGGCCAAUAAUUUGGCCAACACGGCAACAGCCAAGACAACAAC--------CAACAAGAAUUAAG
....((((((.((((.....(((....)))((((((...))))))...).)))((((((....)))))).....(((....)))..)).))))..--------.............. ( -29.40)
>DroYak_CAF1 2283 103 + 1
GAAGUUUUUCGCGCUAAAAAUGCUACGGCUCAAUGGGUUCCACUGCAAGAACCGGCAAACAAUUUGGCCA------CAGCAGCCAAAAGUUCAAA--------GAACUAGAUUUCUG
(((((((.....(((......((....))......(((((........))))))))......((((((..------.....))))))(((((...--------)))))))))))).. ( -24.50)
>DroAna_CAF1 2065 105 + 1
GAAAUUUUCCGGGCCAAGAACGCAACAGCCCAAUGGGUUCCACUACAAGAGCCGGCAACCAACUUGGCCA------ACACAGCCAA--GUCCACAACCAACCGCAACUAGCUU----
.........((((((......((....))......(((((........)))))))).....(((((((..------.....)))))--))..........)))..........---- ( -24.70)
>consensus
GAAAUUUUUCGGGCCAAAAAUGCUACGGCUCAAUGGGUUCCACUGCAAGAACCGGCAAACAAUUUGGCCA______CAACAGCCAAAAGUUCAAA________GAACUAGAAUUCUG
...........((((......((....))......(((((........))))))))).....((((((.............)))))).............................. (-15.12 = -16.29 +   1.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,599,224 – 17,599,329
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 83.12
Mean single sequence MFE -24.34
Consensus MFE -11.74
Energy contribution -14.22
Covariance contribution 2.48
Combinations/Pair 1.16
Mean z-score -2.44
Structure conservation index 0.48
SVM decision value 0.13
SVM RNA-class probability 0.597094
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17599224 105 - 22407834
GGAUAUUUUGGUAUUUUUUUAUCGCCUGCAACCGAGUACACACACAUCCUUAGAAAUAAGGAUGACAUCUGUGGAAAUACUGAAAAAAAUACCUUUACAAUAAUA
.........(((((((((((.(((........)))(((..((((((((((((....)))))))).....))))....)))..)))))))))))............ ( -25.90)
>DroSec_CAF1 4443 103 - 1
GGAUAUUUCGGUAUUU-UUUAUCGCCAGGAAACCAGUACACACACAUCGUUGGAAACUAGGAUGGCAUCUGUGGAAAUACUGGAA-AAAUACCUUUACAAAAAUA
.........(((((((-(((.......(....)(((((..((((((((.(.(....).).)))).....))))....))))))))-)))))))............ ( -25.00)
>DroSim_CAF1 4374 103 - 1
GGAUAUUUCGGUAUUU-UUUAUCGCCAGGAACCCAGUACACACACAUCCUUGGAAACUAGGAUGGCAUCUGUGGAAAUACUGGAA-AAAUACCUUUACAAAAAUA
.........(((((((-((..((.....))..((((((..((((((((((.(....).)))))).....))))....))))))))-)))))))............ ( -28.80)
>DroEre_CAF1 2768 92 - 1
----------GUACU--UCAAUCGGCUAGAACCGACUGCACAUACAUCCUUAGAAACUAGGAUGGCAUCUGAGGAAAUACUGGAG-AAAUACCUUUACAAUAUUA
----------...((--(((.((((......))))...........((((((((..((.....))..)))))))).....)))))-................... ( -18.80)
>DroYak_CAF1 2386 102 - 1
GGAUAUUUUGGUAUU--UUAAUCGACUAGAACCGAGUACACACACAUCCUUUGAAACUAGGAUGGCAUCGGUGGAAAUACUGGAA-AAAUACUUUUACAAUAAUG
.....(((..(((((--((..((.....))(((((((....)).((((((........))))))...))))).)))))))..)))-................... ( -23.20)
>consensus
GGAUAUUUCGGUAUUU_UUUAUCGCCUGGAACCGAGUACACACACAUCCUUAGAAACUAGGAUGGCAUCUGUGGAAAUACUGGAA_AAAUACCUUUACAAUAAUA
.........(((((((((((.(((........)))...((((..((((((.(....).)))))).....)))).........)))))))))))............ (-11.74 = -14.22 +   2.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,599,249 – 17,599,366
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 81.51
Mean single sequence MFE -29.58
Consensus MFE -15.40
Energy contribution -17.56
Covariance contribution 2.16
Combinations/Pair 1.13
Mean z-score -2.15
Structure conservation index 0.52
SVM decision value 0.26
SVM RNA-class probability 0.658841
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17599249 117 - 22407834
GCCACCAUCGAUGUCUCUUUUGAGACACAAGGCAAAAGGAUAUUUUGGUAUUUUUUUAUCGCCUGCAACCGAGUACACACACAUCCUUAGAAAUAAGGAUGACAUCUGUGGAAAUAC
.((((..(((.((((((....))))))..((((((((((((((....))))))))))...)))).....))).........((((((((....))))))))......))))...... ( -37.00)
>DroSec_CAF1 4467 115 - 1
GCCACCAUCGAUGUUCCUUUUGAGA-ACACGGCAAACGGAUAUUUCGGUAUUU-UUUAUCGCCAGGAAACCAGUACACACACAUCGUUGGAAACUAGGAUGGCAUCUGUGGAAAUAC
....((((.(((((((((..((...-.)).(((.....((....))((((...-..)))))))))))..............((((.(.(....).).))))))))).))))...... ( -26.70)
>DroSim_CAF1 4398 116 - 1
GCCACCAUCGAUGUCUCCUUUGAGACACAAGGCAAACGGAUAUUUCGGUAUUU-UUUAUCGCCAGGAACCCAGUACACACACAUCCUUGGAAACUAGGAUGGCAUCUGUGGAAAUAC
....((((.(((((.(((((((.....)))(((.....((....))((((...-..)))))))))))..............((((((.(....).))))))))))).))))...... ( -32.10)
>DroEre_CAF1 2792 105 - 1
GCAACCAUGAAUGUAUCUUAUGAGACACAAUCCAAAA----------GUACU--UCAAUCGGCUAGAACCGACUGCACAUACAUCCUUAGAAACUAGGAUGGCAUCUGAGGAAAUAC
(((....((((.(((.(((.((.((.....)))).))----------)))))--))).((((......)))).))).......((((((((..((.....))..))))))))..... ( -23.40)
>DroYak_CAF1 2410 115 - 1
GCAACCAUUAAUGUCUCUUAUGAGACACAAUCCAACAGGAUAUUUUGGUAUU--UUAAUCGACUAGAACCGAGUACACACACAUCCUUUGAAACUAGGAUGGCAUCGGUGGAAAUAC
...((((....((((((....))))))..((((....))))....))))(((--((..((.....))(((((((....)).((((((........))))))...))))).))))).. ( -28.70)
>consensus
GCCACCAUCGAUGUCUCUUUUGAGACACAAGGCAAAAGGAUAUUUCGGUAUUU_UUUAUCGCCUGGAACCGAGUACACACACAUCCUUAGAAACUAGGAUGGCAUCUGUGGAAAUAC
....((((.(((((.(((((((..........)))))))..........................................((((((.(....).))))))))))).))))...... (-15.40 = -17.56 +   2.16)

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 12:08:05 2006