Locus 1471

Sequence ID 2R_DroMel_CAF1
Location 5,617,805 – 5,617,990
Length 185
Max. P 0.987986
window2505 window2506

overview

Window 5

Location 5,617,805 – 5,617,925
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -28.50
Consensus MFE -27.32
Energy contribution -27.04
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -1.33
Structure conservation index 0.96
SVM decision value 1.06
SVM RNA-class probability 0.908854
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5617805 120 + 20766785
GGGUAAAAUGCAGCCAACACAUCCCAUCCGUUUGGGUCUGGCCCUUAACUUCUCAGUCUUCUACUAUGAGAUUUUGAACUCACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAA
.(((((...((............(((......)))((((((...((((..(((((...........)))))..)))).....))))))...))))))).(((((((.....))))))).. ( -27.70)
>DroVir_CAF1 12297 120 + 1
GGGCAAAAUGCAGCCAACACAUCCCAUCCGCUUGGGUCUUGCACUUAACUUCUCAGUCUUCUAUUAUGAGAUUUUGAAUUCUCCAGAUAAGGCUUGCCAAUUGGCUAAACAGGUUAAUAU
.((((......((((....((.((((......))))...))...((((..(((((...........)))))..)))).............)))))))).(((((((.....))))))).. ( -25.80)
>DroSec_CAF1 7470 120 + 1
GGGUAAAAUGCAGCCAACACAUCCCAUCCGUUUGGGUCUGGCCCUUAACUUCUCAGUCUUCUACUAUGAGAUUUUGAACUCACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAA
.(((((...((............(((......)))((((((...((((..(((((...........)))))..)))).....))))))...))))))).(((((((.....))))))).. ( -27.70)
>DroSim_CAF1 9098 120 + 1
GGGUAAAAUGCAGCCAACACAUCCCAUCCGUUUGGGUCUGGCCCUUAACUUCUCAGUCUUCUACUAUGAGAUUUUGAACUCACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAA
.(((((...((............(((......)))((((((...((((..(((((...........)))))..)))).....))))))...))))))).(((((((.....))))))).. ( -27.70)
>DroAna_CAF1 8008 120 + 1
GGGUAAAAUGCAGCCAACACAUCCCAUCCGUUUGGGUCUGGCCCUCAACUUCUCAGUCUUCUACUAUGAGAUUUUGAACUCGCCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAA
.(((((...((............(((......)))(((((((..((((..(((((...........)))))..))))....)))))))...))))))).(((((((.....))))))).. ( -33.60)
>consensus
GGGUAAAAUGCAGCCAACACAUCCCAUCCGUUUGGGUCUGGCCCUUAACUUCUCAGUCUUCUACUAUGAGAUUUUGAACUCACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAA
.(((((...((............(((......)))((((((...((((..(((((...........)))))..)))).....))))))...))))))).(((((((.....))))))).. (-27.32 = -27.04 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,617,885 – 5,617,990
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.06
Mean single sequence MFE -24.12
Consensus MFE -16.92
Energy contribution -17.46
Covariance contribution 0.54
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.70
SVM decision value 2.10
SVM RNA-class probability 0.987986
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5617885 105 + 20766785
CACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAACA-CACU---GAGACUUGGCUCGAUUAAUC---GAAAUGUAUGGCAAGCGAGCAAGAAAGGCACACAAAAUC--------
...........((((((((....(((((.(((((.......)-).))---)....)))))((((....))---))......))))))))..((.......))..........-------- ( -23.00)
>DroVir_CAF1 12377 93 + 1
CUCCAGAUAAGGCUUGCCAAUUGGCUAAACAGGUUAAUAUUC-AAGU---G------------------C---CAAUUGUCUGGCAGGCGAGC--AAGAGUCAAGCCAAGUGCAACAACA
.....(((...(((((((.(((((((.....)))))))....-...(---(------------------(---((......))))))))))))--....)))..((.....))....... ( -26.10)
>DroSec_CAF1 7550 103 + 1
CACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAACA-GACU---GAGAUUUGGCUCGAUUAAUC---GAAAUGUAUGGCAAGCGAGC--GAAAGGCACACAAAAUU--------
...........((((((((....((((((..((((.......-))))---....))))))((((....))---))......))))))))..((--.....))..........-------- ( -25.20)
>DroSim_CAF1 9178 103 + 1
CACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAACA-CACU---GAGACUUGGCUCGAUUAAUC---GAAAUGUAUGGCAAGCGAGC--GAAAGGCACACAAAAUU--------
...........((((((((....(((((.(((((.......)-).))---)....)))))((((....))---))......))))))))..((--.....))..........-------- ( -23.50)
>DroAna_CAF1 8088 101 + 1
CGCCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAAUAAUACUAUCAAGGCU---AUCCAUUAAUUUGAGAAAUGUAUGGCAAGCA--------AGGCACAAAAAACA--------
.(((.......(((((((.(((((((.....)))))))....((((..(((((..(---(.....)).))))).....))))))))))).--------.)))..........-------- ( -22.80)
>consensus
CACCAGACAAAGCUUGCCAAUUGGCUAAACAGGUUAAUAACA_CACU___GAGACUUGGCUCGAUUAAUC___GAAAUGUAUGGCAAGCGAGC__GAAAGGCACACAAAAUU________
...........(((((((((((((((.....)))))))............(((......)))...................))))))))............................... (-16.92 = -17.46 +   0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:39 2006