Locus 300

Sequence ID 2R_DroMel_CAF1
Location 2,017,699 – 2,017,867
Length 168
Max. P 0.987504
window618 window619 window620 window621

overview

Window 8

Location 2,017,699 – 2,017,800
Length 101
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 86.13
Mean single sequence MFE -28.57
Consensus MFE -19.08
Energy contribution -19.57
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.67
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2017699 101 + 20766785
AUCUCGUUUAAGUGACUCCGAAACGGCAGCACUGCAACAGC------------AACAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAG
.((((((...((((.(((((...))).))))))(((((.((------------((..((....))..)))).))))).......((((.....)))))))).))......... ( -27.20)
>DroSec_CAF1 2733 107 + 1
AUCUCGUUUAAGUGACUCCGAAACGGCAGCACUGCAACAGCAACUGCAA------CAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAG
...(((((..((((.(((((...))).))))))((....((((((((((------..((....))..)))))))))).......((((.....)))))))))))......... ( -33.90)
>DroSim_CAF1 2800 113 + 1
AUCUCGUUUAAGUGACUCCGAAACGGCAGCACUGCAACAGCAACUGCAACAGCAACAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUAGAAAG
...(((((..((((.(((((...))).))))))((....((((((((((..((..........))..)))))))))).......((((.....)))))))))))......... ( -33.00)
>DroEre_CAF1 2765 89 + 1
AUCUCGUUUAAGUGACUCCGAAGCGGCAGCA------------------------CAGCACCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAG
.((((((....(((.(((((...))).))))------------------------).((....((.(((((....)))))....))(....)...)))))).))......... ( -20.20)
>consensus
AUCUCGUUUAAGUGACUCCGAAACGGCAGCACUGCAACAGC______________CAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAG
.((((((...((((.(((((...))).))))))........................((....((.(((((....)))))....))(....)...)))))).))......... (-19.08 = -19.57 +   0.50) 

alignment

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secondary structure

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dotplot

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Window 9

Location 2,017,738 – 2,017,838
Length 100
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 89.08
Mean single sequence MFE -31.62
Consensus MFE -26.71
Energy contribution -26.53
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.80
Structure conservation index 0.84
SVM decision value 2.08
SVM RNA-class probability 0.987504
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2017738 100 + 20766785
GC------------AACAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCU
((------------(...((((..((((((((((((((.......)))))..((((....))))(((.(....))))............)))))))))..)))).))).... ( -30.70)
>DroSec_CAF1 2772 106 + 1
GCAACUGCAA------CAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCA
((((((((((------..((....))..))))))))))....(((..(((((((((....))))..........((((((.......)))))).)))))..)))........ ( -33.60)
>DroSim_CAF1 2839 112 + 1
GCAACUGCAACAGCAACAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUAGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCA
((((((((((..((..........))..))))))))))....(((..(((((((((....))))..........((((((.......)))))).)))))..)))........ ( -32.70)
>DroEre_CAF1 2796 96 + 1
----------------CAGCACCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUUUGUAUCU
----------------.(((((..((((((((((((((.......)))))..((((....))))(((.(....))))............)))))))))..)))))....... ( -29.50)
>consensus
GC______________CAGCAUCAGCAAUUGCAGUUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCA
..................((((..((((((((((((((.......)))))..((((....))))((((.....))))............)))))))))..))))........ (-26.71 = -26.53 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 0

Location 2,017,738 – 2,017,838
Length 100
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 89.08
Mean single sequence MFE -28.55
Consensus MFE -21.42
Energy contribution -21.68
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.75
SVM decision value 0.65
SVM RNA-class probability 0.810500
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2017738 100 - 20766785
AGAUACACACACUGGCAAUUGCAACUUAUUAUAUUACACUUUCGAUGUCAUCGCGCGAUGUUGCCGCUGUCAUUGCAACUGCAAUUGCUGAUGCUGUU------------GC
......(((((..((((((((((...((......))......(((((.((.((.(((....))))).)).)))))....))))))))))..)).))).------------.. ( -24.30)
>DroSec_CAF1 2772 106 - 1
UGAUACACACACUGGCAAUUGCAACUUAUUAUAUUACACUUUCGAUGUCAUCGCGCGAUGUUGCCGCUGUCAUUGCAACUGCAAUUGCUGAUGCUG------UUGCAGUUGC
........(((.((((((............(((((........)))))((((....)))))))))).)))....(((((((((((.((....)).)------)))))))))) ( -30.60)
>DroSim_CAF1 2839 112 - 1
UGAUACACACACUGGCAAUUGCAACUUAUUAUAUUACACUUUCUAUGUCAUCGCGCGAUGUUGCCGCUGUCAUUGCAACUGCAAUUGCUGAUGCUGUUGCUGUUGCAGUUGC
..............(((((((((((...................(((.((.((.(((....))))).)).))).(((((.(((........))).))))).))))))))))) ( -31.40)
>DroEre_CAF1 2796 96 - 1
AGAUACAAACACUGGCAAUUGCAACUUAUUAUAUUACACUUUCGAUGUCAUCGCGCGAUGUUGCCGCUGUCAUUGCAACUGCAAUUGCUGGUGCUG----------------
.........(((..(((((((((...((......))......(((((.((.((.(((....))))).)).)))))....)))))))))..)))...---------------- ( -27.90)
>consensus
AGAUACACACACUGGCAAUUGCAACUUAUUAUAUUACACUUUCGAUGUCAUCGCGCGAUGUUGCCGCUGUCAUUGCAACUGCAAUUGCUGAUGCUG______________GC
.........((..((((((((((...((......))......(((((.((.((.(((....))))).)).)))))....))))))))))..))................... (-21.42 = -21.68 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 1

Location 2,017,760 – 2,017,867
Length 107
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 95.48
Mean single sequence MFE -35.38
Consensus MFE -33.33
Energy contribution -33.20
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.93
Structure conservation index 0.94
SVM decision value 1.09
SVM RNA-class probability 0.912810
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2017760 107 + 20766785
UUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCUCCGUUUGUUGCCGCGGGUCGUGCACUCAG
.((((.((((.(((((((((.((.(.(((((((((....)((((((.......)))))).........)))).)))).)))..)))))))))..))))))))..... ( -36.90)
>DroSec_CAF1 2800 107 + 1
UUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCACCGUUGGUUGCCGCGGGUCGUGCACUCAG
.((((.((((.((((((((..((.(.(((((((((....)((((((.......)))))).........)))).)))).)))...))))))))..))))))))..... ( -36.70)
>DroSim_CAF1 2873 107 + 1
UUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUAGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCACCGUUGGUUGCCGCGGGUCGUGCACUCAG
.((((.((((.((((((((..((.(.((((((((((....((((((.......))))))....)...))))).)))).)))...))))))))..))))))))..... ( -37.20)
>DroEre_CAF1 2814 107 + 1
UUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUUUGUAUCUCCUUUUGUUGCCGUGGGUCGUGUACUUGG
.((((.((((.(((((((((((....))))....((((((.(..((((((......((....))......))))))..))))))))))))))..))))))))..... ( -30.70)
>consensus
UUGCAAUGACAGCGGCAACAUCGCGCGAUGACAUCGAAAGUGUAAUAUAAUAAGUUGCAAUUGCCAGUGUGUGUAUCACCGUUGGUUGCCGCGGGUCGUGCACUCAG
.((((.((((.((((((((..((.(.((((((((.(.((.((((((.......)))))).))..).))))...)))).)))...))))))))..))))))))..... (-33.33 = -33.20 +  -0.13) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:56 2006