Locus 4333

Sequence ID 3R_DroMel_CAF1
Location 11,456,565 – 11,456,790
Length 225
Max. P 0.998980
window7082 window7083 window7084

overview

Window 2

Location 11,456,565 – 11,456,685
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -27.42
Consensus MFE -26.46
Energy contribution -26.22
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -1.32
Structure conservation index 0.96
SVM decision value 0.76
SVM RNA-class probability 0.842455
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11456565 120 + 27905053
UAUUAACAGCAACGUAAUCUGAAUGCGAAAUCAAGUCGCAGUGUACAGCCCACAAUAUCAGUUGACAACUGUCGACGGUCGUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAAC
.............(((((((((.(((((.......)))))(((.......)))....))))..(((.((((....)))).)))((((((((........))))))))..)))))...... ( -27.30)
>DroSec_CAF1 189053 120 + 1
UAUUAACAGCAACGUAAUCUGAAUGCGAAAUCAAGUUGCAGUGCACAGCCCACAAUAUCAGUUGACAACUGUCGACGGUCGUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAAC
........(((..((((..(((........)))..))))..)))................((((((....)))))).......((((((((........))))))))............. ( -27.90)
>DroSim_CAF1 184137 120 + 1
UAUUAACAGCAACGUAAUCUGAAUGCGAAAUCAAGUUGCAGUGCACAGCCCACAAUAUCAGUUGACAACUGUCGACGGUCGUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAAC
........(((..((((..(((........)))..))))..)))................((((((....)))))).......((((((((........))))))))............. ( -27.90)
>DroEre_CAF1 178263 120 + 1
UAUUAGCAACAACGUAAUCUGAAUGCGAAAUCAAGUCGCAGUGCACAGCCCACAAUAUCAGUUGACAACUGUCGACGGUCGUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAAC
.............(((((((((.(((((.......)))))(((.......)))....))))..(((.((((....)))).)))((((((((........))))))))..)))))...... ( -27.00)
>DroYak_CAF1 182135 120 + 1
UAUUAGCAACAACGUAAUCUGAAUGCGAAAUCAAGUCGCAGUGCACAGUCCACAAUAUCAGUUGACAACUGUCGACGGUCGUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAAC
.............(((((((((.(((((.......)))))(((.......)))....))))..(((.((((....)))).)))((((((((........))))))))..)))))...... ( -27.00)
>consensus
UAUUAACAGCAACGUAAUCUGAAUGCGAAAUCAAGUCGCAGUGCACAGCCCACAAUAUCAGUUGACAACUGUCGACGGUCGUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAAC
.............(((((((((.(((((.......)))))(((.......)))....))))..(((.((((....)))).)))((((((((........))))))))..)))))...... (-26.46 = -26.22 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,456,645 – 11,456,765
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -38.82
Consensus MFE -33.00
Energy contribution -33.40
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -2.80
Structure conservation index 0.85
SVM decision value 3.31
SVM RNA-class probability 0.998980
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11456645 120 + 27905053
GUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAACUGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCUACGGUUUCCUUUAAAGUGCAGCAAUACACUAAGCCAA
...((((((((........)))))))).............((((((..((((.(((((((((((..((....)).)))))))..))))...)))).....)))))).............. ( -35.50)
>DroSec_CAF1 189133 120 + 1
GUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAACUGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACAGCCUCCUUUAAAGUGCAGCAAUACACUAAGCAAA
...((((((((........)))))))).............((((........(((.((((((((..((....)).))))))))...((((.......)).)).)))........)))).. ( -35.19)
>DroSim_CAF1 184217 120 + 1
GUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAACUGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACGGCCUCCUUUAAAGUGCAGCAAUACACUAAGCAAA
...((((((((........)))))))).............((((...((.((.(((((((((((..((....)).))))))))..))))).))....((((.(....).)))).)))).. ( -37.40)
>DroEre_CAF1 178343 119 + 1
GUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAACUGCUGUCAGAAGUGC-GGCGGGAACUAGGCAACUUUUUCCGCCACUGUGCUCCUUAAAGUGCAGAAGUACACUGAGCCAA
...((((((((........))))))))..............((..((((..((((-((((((((..((....)).)))))))).(((..((......))..)))..)))).))))))... ( -43.10)
>DroYak_CAF1 182215 120 + 1
GUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAACUGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACGGUCUUCUUUAAAGUGCAGCAGUGCACUGAGCCAA
...((((((((........))))))))...........((((((((.(((((.(((((((((((..((....)).))))))))..)))))))).......))))))))((.....))... ( -42.90)
>consensus
GUCUGGCAGGCAUUUAAACGCUUGUCAAAAUUAUAUAAACUGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACGGUCUCCUUUAAAGUGCAGCAAUACACUAAGCCAA
...((((((((........)))))))).............((((((..((((.(((((((((((..((....)).))))))))..)))...)))).....)))))).............. (-33.00 = -33.40 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,456,685 – 11,456,790
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.06
Mean single sequence MFE -31.80
Consensus MFE -22.54
Energy contribution -22.54
Covariance contribution -0.00
Combinations/Pair 1.16
Mean z-score -1.67
Structure conservation index 0.71
SVM decision value 0.14
SVM RNA-class probability 0.605051
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11456685 105 + 27905053
UGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCUACGGUUUCCUUUAAAGUGCAGCAAUACACUAAGCCAAAAACUAACCAAAGAUGCU--GGCUACU-------------
((((((..((((.(((((((((((..((....)).)))))))..))))...)))).....))))))........(((((..(.((......)).)..)--))))...------------- ( -30.70)
>DroSec_CAF1 189173 105 + 1
UGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACAGCCUCCUUUAAAGUGCAGCAAUACACUAAGCAAAAAACUAACUAAAGAUGCA--GGCUACU-------------
.(((......)))...((((((((..((....)).))))))))..(((((.......((((.(....).))))..(((................))))--))))...------------- ( -26.89)
>DroSim_CAF1 184257 105 + 1
UGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACGGCCUCCUUUAAAGUGCAGCAAUACACUAAGCAAAAAACCAACUAAAGAUGCA--GGCGACU-------------
....(((.........((((((((..((....)).))))))))...((((.......((((.(....).))))..(((................))))--)))))).------------- ( -28.19)
>DroEre_CAF1 178383 106 + 1
UGCUGUCAGAAGUGC-GGCGGGAACUAGGCAACUUUUUCCGCCACUGUGCUCCUUAAAGUGCAGAAGUACACUGAGCCAAAAACGAGCCAAGGAUGUA--GGCUGAUGC-----------
.((.(((((..((((-((((((((..((....)).)))))))).(((..((......))..)))..)))).(((..((.............))...))--).)))))))----------- ( -37.02)
>DroYak_CAF1 182255 120 + 1
UGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACGGUCUUCUUUAAAGUGCAGCAGUGCACUGAGCCAAAAACUAACUAAAGAUGUAAAGACUAAAGCGUAACUACAGC
.(((((.((...(((.((((((((..((....)).))))))))..(((((((((((.((((((....)))))).((.......))...)))))).....)))))...)))...))))))) ( -36.20)
>consensus
UGCUGUCAGAAGUGCCGGCGGGAACUAGGGAACUUUUUCCGCCACGGUCUCCUUUAAAGUGCAGCAAUACACUAAGCCAAAAACUAACUAAAGAUGCA__GGCUACU_____________
((((((..((((.(((((((((((..((....)).))))))))..)))...)))).....)))))).............................((....))................. (-22.54 = -22.54 +  -0.00)

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 11:26:31 2006