Locus 2421

Sequence ID 2L_DroMel_CAF1
Location 6,610,155 – 6,610,302
Length 147
Max. P 0.988407
window3894 window3895 window3896

overview

Window 4

Location 6,610,155 – 6,610,262
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.23
Mean single sequence MFE -28.62
Consensus MFE -21.42
Energy contribution -22.86
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.75
SVM decision value 0.52
SVM RNA-class probability 0.766805
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6610155 107 + 22407834
AAAAUACAAAU----------AAGCCUGCACUUUGACUGCUAGUUGACCCAUAAAUAAAUCAUUUCCGCAA---GCAAAGCGCUGUUGCAUAAUAGAUGCAACGGAUUUAUGUGCGGUAA
...........----------..(((.((((.(..((.....))..).......(((((((.....(((..---.....))).((((((((.....)))))))))))))))))))))).. ( -26.60)
>DroSec_CAF1 37383 110 + 1
AAAAUACAAAU----------GAGCCUGCACUUUGACUGCCAGUUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCAGUUGCAUAAUAGAUGCAGCGGAUUUAUGUGCGGUAA
...........----------..(((.((((.(..((.....))..).......(((((((.....(((..........)))..(((((((.....))))))).)))))))))))))).. ( -26.10)
>DroSim_CAF1 38607 110 + 1
AAAAUACAAAU----------GAGCCUGCACUUUGACUGCCAGUUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUAGAUGCAGCGGAUUUAUGUGCGGUAA
...........----------..(((.((((.(..((.....))..).................(((((.((((((.....))))))((((.....)))).))))).....))))))).. ( -30.10)
>DroEre_CAF1 38567 119 + 1
AAAAUACAAAUGAGCUGAGUUGAGCUUGCACUUUGACUGCUAGCUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUAGAUG-UGCGGAUUUAUGUGCGGUAA
.......((((((..((.(((.((((.(((.......))).))))))).))........))))))(((((((((((.....))))))(((((.....))-))).........)))))... ( -29.50)
>DroYak_CAF1 39133 120 + 1
AAAAUACAAAUUUGCUGAGUUGAGCCUGCACUUUGACUGCUAGGUGACCCAUUAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUGAAUGCCGCGGAUUUAUGUGCGGUAA
...........(((.((.(((..(((((((.......))).))))))).)).)))....(((((...((((.((((.....))))))))..))))).(((((((.(....).))))))). ( -30.80)
>consensus
AAAAUACAAAU__________GAGCCUGCACUUUGACUGCUAGUUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUAGAUGCAGCGGAUUUAUGUGCGGUAA
.......................(((.((((.(((((.....))))).................(((((.((((((.....))))))((((.....)))).))))).....))))))).. (-21.42 = -22.86 +   1.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,610,155 – 6,610,262
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.23
Mean single sequence MFE -31.04
Consensus MFE -23.28
Energy contribution -24.12
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.75
SVM decision value 1.10
SVM RNA-class probability 0.914559
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6610155 107 - 22407834
UUACCGCACAUAAAUCCGUUGCAUCUAUUAUGCAACAGCGCUUUGC---UUGCGGAAAUGAUUUAUUUAUGGGUCAACUAGCAGUCAAAGUGCAGGCUU----------AUUUGUAUUUU
.....(((.((((..(((((((((.....))))))).((((((((.---((((.....(((((((....)))))))....)))).)))))))).)).))----------)).)))..... ( -32.80)
>DroSec_CAF1 37383 110 - 1
UUACCGCACAUAAAUCCGCUGCAUCUAUUAUGCAACUGCGCUUUGCUGUUUGCGGAAAUGAUUUAUUUAUGGGUCAACUGGCAGUCAAAGUGCAGGCUC----------AUUUGUAUUUU
.........((((((..(((((((.....))))).((((((((((((((..(..((.((((.....))))...))..)..)))).))))))))))))..----------))))))..... ( -32.70)
>DroSim_CAF1 38607 110 - 1
UUACCGCACAUAAAUCCGCUGCAUCUAUUAUGCAACAGCGCUUUGCUGUUUGCGGAAAUGAUUUAUUUAUGGGUCAACUGGCAGUCAAAGUGCAGGCUC----------AUUUGUAUUUU
.........((((((..(((((((.....))))....((((((((((((..(..((.((((.....))))...))..)..)))).)))))))).)))..----------))))))..... ( -29.20)
>DroEre_CAF1 38567 119 - 1
UUACCGCACAUAAAUCCGCA-CAUCUAUUAUGCAACAGCGCUUUGCUGUUUGCGGAAAUGAUUUAUUUAUGGGUCAGCUAGCAGUCAAAGUGCAAGCUCAACUCAGCUCAUUUGUAUUUU
.....((..........)).-........((((((..(((((((((((((.((.((.((((.....))))...)).)).))))).)))))))).((((......))))...))))))... ( -29.00)
>DroYak_CAF1 39133 120 - 1
UUACCGCACAUAAAUCCGCGGCAUUCAUUAUGCAACAGCGCUUUGCUGUUUGCGGAAAUGAUUUAUUAAUGGGUCACCUAGCAGUCAAAGUGCAGGCUCAACUCAGCAAAUUUGUAUUUU
...((((..........))))........((((((..(((((((((((((...((...(((((((....))))))))).))))).))))))))..(((......)))....))))))... ( -31.50)
>consensus
UUACCGCACAUAAAUCCGCUGCAUCUAUUAUGCAACAGCGCUUUGCUGUUUGCGGAAAUGAUUUAUUUAUGGGUCAACUAGCAGUCAAAGUGCAGGCUC__________AUUUGUAUUUU
.....((((.....(((((.((((.....))))((((((.....)))))).)))))..(((((((....))))))).............))))........................... (-23.28 = -24.12 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,610,185 – 6,610,302
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -30.06
Consensus MFE -25.74
Energy contribution -26.14
Covariance contribution 0.40
Combinations/Pair 1.12
Mean z-score -2.01
Structure conservation index 0.86
SVM decision value 2.12
SVM RNA-class probability 0.988407
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6610185 117 + 22407834
UAGUUGACCCAUAAAUAAAUCAUUUCCGCAA---GCAAAGCGCUGUUGCAUAAUAGAUGCAACGGAUUUAUGUGCGGUAAUGUUGUCUAAAAUAUGCAUAAGUCGUAACCGUCGAUUUAA
.(((((((............((((.(((((.---..(((...(((((((((.....))))))))).)))...))))).))))..........(((((....).))))...)))))))... ( -29.30)
>DroSec_CAF1 37413 120 + 1
CAGUUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCAGUUGCAUAAUAGAUGCAGCGGAUUUAUGUGCGGUAAUGUUGCCUAAAAAAUGCAUAAGUCGUAACCGUCGAUUUAA
...............((((((...(((((.....((.....))...(((((.....)))))))))).......(((((.(((.(((.........))).....))).))))).)))))). ( -27.00)
>DroSim_CAF1 38637 120 + 1
CAGUUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUAGAUGCAGCGGAUUUAUGUGCGGUAAUGUUGCCUAAAAUAUGCAUAAGUCGUAACCGUCGAUUUAA
...............((((((...(((((.((((((.....))))))((((.....)))).))))).......(((((.(((.(((.........))).....))).))))).)))))). ( -32.00)
>DroEre_CAF1 38607 119 + 1
UAGCUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUAGAUG-UGCGGAUUUAUGUGCGGUAAUGUUGCCUAAAAUAUGCAUAAGUUAUAACCGUCGAUUUAA
...............((((((...(((((.((((((.....))))))((((.....)))-)))))).......(((((.(((.(((.........))).....))).))))).)))))). ( -28.20)
>DroYak_CAF1 39173 120 + 1
UAGGUGACCCAUUAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUGAAUGCCGCGGAUUUAUGUGCGGUAAUGUUGUCUAAAAUAUGCAUAAGUUGUAACCGCCGAUUUAA
..(....).......((((((...(((((.((((((.....))))))((((.....)))).))))).....(.(((((..((((......))))((((.....)))))))))))))))). ( -33.80)
>consensus
UAGUUGACCCAUAAAUAAAUCAUUUCCGCAAACAGCAAAGCGCUGUUGCAUAAUAGAUGCAGCGGAUUUAUGUGCGGUAAUGUUGCCUAAAAUAUGCAUAAGUCGUAACCGUCGAUUUAA
...............((((((...(((((.((((((.....))))))((((.....)))).))))).......(((((.(((.(((.........))).....))).))))).)))))). (-25.74 = -26.14 +   0.40)

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 10:27:39 2006