Locus 6632

Sequence ID 2R_DroMel_CAF1
Location 20,723,341 – 20,723,450
Length 109
Max. P 0.959156
window10561 window10562

overview

Window 1

Location 20,723,341 – 20,723,450
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.25
Mean single sequence MFE -30.32
Consensus MFE -22.80
Energy contribution -22.36
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -2.56
Structure conservation index 0.75
SVM decision value 1.50
SVM RNA-class probability 0.959156
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20723341 109 + 20766785
UAAUAAUCGCACAUCCUGUGCGCAUACA------UACUAUUCGGUGUU-----UUUGUGGUUUUGGUUUUCAUUGUGAAAGUGAAAACACAGAAGCGGAUGCACUUUAUAGAGUUGUUUU
.(((((((((((.....)))))......------..((((..(((((.-----(((((..((((((((((((((.....))))))))).)))))))))).)))))..)))).)))))).. ( -32.40)
>DroSec_CAF1 156724 116 + 1
UGAUAAUCGCACAUCCUGUGAGCAUACAU----AUACUAUUCGGUGUUUUAUUUUUGUGGUUUUGGUUUUCAUUGUGAAAGUGAAAACACAGAAGCGGAUGCACUUUAUAGAGUUCUUCU
......(((((.....)))))........----...((((..(((((((..((((((((.((((..(((((.....)))))..))))))))))))..)).)))))..))))......... ( -26.30)
>DroSim_CAF1 161808 120 + 1
UAAUAAUCGCACAUCCUGUGAGCAUACAUAUGUAUACUAUUCGGUGUUUUAUUUUUGUGGUUUUGGUUUUCAUUGUGAAAGUGAAAACACAGAAGCGGAUGCACUUUAUAGAGUUCUUCU
...................((((((((....)))).((((..(((((((..((((((((.((((..(((((.....)))))..))))))))))))..)).)))))..)))).)))).... ( -28.00)
>DroEre_CAF1 197786 114 + 1
UUAUAAUCGCACAUCCUGUG--CAUACAU----AUACUAUUUGGUGUUUUGUUUUUGUGGUUUUGGUUUUCAUUGUAAAAGUGAAAACACAAAAACGGAUGCACUUUAUACAUAUGAUCA
........((((.....)))--)...(((----((..(((..((((((((((((((((.......(((((((((.....)))))))))))))))))))).)))))..))).))))).... ( -31.81)
>DroYak_CAF1 163018 114 + 1
UAAUAAUCGCACAUCCUGUG--CAUACAU----AUACUAUUUGGUGUUCUGUUUUUGUGGUUUUGGUUUUCAUUGUGAAAGUGAAAACACAAGAACGGAUGCACUUUAUACAGCUGAUCG
.....(((((((.....)))--)......----....(((..(((((((((((((((((.((((..(((((.....)))))..)))))))))))))))).)))))..))).....))).. ( -33.10)
>consensus
UAAUAAUCGCACAUCCUGUG_GCAUACAU____AUACUAUUCGGUGUUUUAUUUUUGUGGUUUUGGUUUUCAUUGUGAAAGUGAAAACACAGAAGCGGAUGCACUUUAUAGAGUUGUUCU
...........(((((......((((.......(((((....)))))........))))(((((.(((((((((.....)))))))))...))))))))))................... (-22.80 = -22.36 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,723,341 – 20,723,450
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.25
Mean single sequence MFE -22.39
Consensus MFE -17.88
Energy contribution -17.88
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.80
SVM decision value 1.36
SVM RNA-class probability 0.945748
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20723341 109 - 20766785
AAAACAACUCUAUAAAGUGCAUCCGCUUCUGUGUUUUCACUUUCACAAUGAAAACCAAAACCACAAA-----AACACCGAAUAGUA------UGUAUGCGCACAGGAUGUGCGAUUAUUA
................(..(((((..(((.(((((((...((((.....))))............))-----))))).)))..((.------((....)).)).)))))..)........ ( -18.76)
>DroSec_CAF1 156724 116 - 1
AGAAGAACUCUAUAAAGUGCAUCCGCUUCUGUGUUUUCACUUUCACAAUGAAAACCAAAACCACAAAAAUAAAACACCGAAUAGUAU----AUGUAUGCUCACAGGAUGUGCGAUUAUCA
................(..(((((.....((.(((((((.........))))))))).........................(((((----....)))))....)))))..)........ ( -19.50)
>DroSim_CAF1 161808 120 - 1
AGAAGAACUCUAUAAAGUGCAUCCGCUUCUGUGUUUUCACUUUCACAAUGAAAACCAAAACCACAAAAAUAAAACACCGAAUAGUAUACAUAUGUAUGCUCACAGGAUGUGCGAUUAUUA
................(..(((((.....((.(((((((.........))))))))).........................(((((((....)))))))....)))))..)........ ( -24.30)
>DroEre_CAF1 197786 114 - 1
UGAUCAUAUGUAUAAAGUGCAUCCGUUUUUGUGUUUUCACUUUUACAAUGAAAACCAAAACCACAAAAACAAAACACCAAAUAGUAU----AUGUAUG--CACAGGAUGUGCGAUUAUAA
..........(((((.(..((((((((((((((((((((.........))))))).......)))))))).............((((----....)))--)...)))))..)..))))). ( -25.91)
>DroYak_CAF1 163018 114 - 1
CGAUCAGCUGUAUAAAGUGCAUCCGUUCUUGUGUUUUCACUUUCACAAUGAAAACCAAAACCACAAAAACAGAACACCAAAUAGUAU----AUGUAUG--CACAGGAUGUGCGAUUAUUA
................(..((((((((((((((((((...((((.....))))...)))).)))).....)))))........((((----....)))--)...)))))..)........ ( -23.50)
>consensus
AGAACAACUCUAUAAAGUGCAUCCGCUUCUGUGUUUUCACUUUCACAAUGAAAACCAAAACCACAAAAACAAAACACCGAAUAGUAU____AUGUAUGC_CACAGGAUGUGCGAUUAUUA
................(..(((((.....((.(((((((.........)))))))))...................................(((......))))))))..)........ (-17.88 = -17.88 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:43 2006