Locus 2120

Sequence ID 2R_DroMel_CAF1
Location 7,939,369 – 7,939,515
Length 146
Max. P 0.938503
window3512 window3513 window3514 window3515

overview

Window 2

Location 7,939,369 – 7,939,482
Length 113
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 80.34
Mean single sequence MFE -31.69
Consensus MFE -23.34
Energy contribution -23.50
Covariance contribution 0.16
Combinations/Pair 1.26
Mean z-score -2.03
Structure conservation index 0.74
SVM decision value 1.16
SVM RNA-class probability 0.924035
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7939369 113 + 20766785
UUUU-----AGCAAUUUUAAAUUUUAAAAUGCGGUUGCUCAAAAUAAUCUGGCAGCUCUUGCAACCUUAUGGCAUCCGUGCGAACAGCUGUCAGAUCAGCUGUUGUUGUUUCCAGCCC
....-----.(((.(((((.....))))))))(((((.........(((((((((((.(((((.((....))......)))))..)))))))))))((((....))))....))))). ( -32.60)
>DroSec_CAF1 17839 99 + 1
-------------------AAUUUUAAAAUGCGGUUGCUCCAAAUAAUCUGGCAGCUCUUGUAACCUUCUGGCAACGGUGCGGACAGCUUUCAGAUCAGCUGUUGUUGCUGCCAGCCC
-------------------.............((.....)).......((((((((........((..(((....)))...))((((((........))))))....))))))))... ( -29.30)
>DroSim_CAF1 19387 113 + 1
UUUU-----AGCAAUUUCAAAUUUUAAAAUGCGGUUGCUCCAAAUAAUCUGGCAGCUCUUGUAACCUUCUGGCAACGGUGCGGACAGCUGUCAGAUCAGCUGUUGUUGCUGCCAGCCC
....-----((((((..((..........))..)))))).........((((((((........((..(((....)))...))(((((((......)))))))....))))))))... ( -37.30)
>DroEre_CAF1 16269 118 + 1
UUAUAUAUUUGCAAUUUCAAAUUUAAAUAUGCGCUAGUUCCAAAUCAUCUGGCAGCUCUUGGAACCUUCUGGCAUCCGUGUGAACAGCUGUCAGAUCAGCUGUUCUUACUGCCAGCCC
...((((((((.(((.....))))))))))).....(((((((...............)))))))...((((((...(((.(((((((((......))))))))).)))))))))... ( -33.46)
>DroYak_CAF1 23285 117 + 1
UGUAAUAUGUGCAAUUUCAAUUUUAAA-AUGCGGUUGAUCCAAAUUAUCUGGCAUCUCUUGGUACCGUCUGGCAUCCGUGCGAGCAGCUGUCAGAUCAGCUGUUUUUGUCGCUAGCCC
((((.....))))..............-..(((((.((((((.......))).))).......)))))..(((...((...(((((((((......)))))))))....))...))). ( -25.80)
>consensus
UUUU_____AGCAAUUUCAAAUUUUAAAAUGCGGUUGCUCCAAAUAAUCUGGCAGCUCUUGGAACCUUCUGGCAUCCGUGCGAACAGCUGUCAGAUCAGCUGUUGUUGCUGCCAGCCC
................................................((((((((...............(((....))).((((((((......))))))))...))))))))... (-23.34 = -23.50 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,939,369 – 7,939,482
Length 113
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -32.82
Consensus MFE -21.46
Energy contribution -22.34
Covariance contribution 0.88
Combinations/Pair 1.11
Mean z-score -2.24
Structure conservation index 0.65
SVM decision value 1.27
SVM RNA-class probability 0.938503
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7939369 113 - 20766785
GGGCUGGAAACAACAACAGCUGAUCUGACAGCUGUUCGCACGGAUGCCAUAAGGUUGCAAGAGCUGCCAGAUUAUUUUGAGCAACCGCAUUUUAAAAUUUAAAAUUGCU-----AAAA
((((((..........))))(((((((.(((((.((.(((.....(((....)))))))).))))).)))))))..........))((((((((.....))))).))).-----.... ( -31.20)
>DroSec_CAF1 17839 99 - 1
GGGCUGGCAGCAACAACAGCUGAUCUGAAAGCUGUCCGCACCGUUGCCAGAAGGUUACAAGAGCUGCCAGAUUAUUUGGAGCAACCGCAUUUUAAAAUU-------------------
...((((((((....((((((........)))))).......((.(((....))).))....))))))))..........((....))...........------------------- ( -30.10)
>DroSim_CAF1 19387 113 - 1
GGGCUGGCAGCAACAACAGCUGAUCUGACAGCUGUCCGCACCGUUGCCAGAAGGUUACAAGAGCUGCCAGAUUAUUUGGAGCAACCGCAUUUUAAAAUUUGAAAUUGCU-----AAAA
...((((((((....(((((((......))))))).......((.(((....))).))....)))))))).........(((((...((..........))...)))))-----.... ( -35.10)
>DroEre_CAF1 16269 118 - 1
GGGCUGGCAGUAAGAACAGCUGAUCUGACAGCUGUUCACACGGAUGCCAGAAGGUUCCAAGAGCUGCCAGAUGAUUUGGAACUAGCGCAUAUUUAAAUUUGAAAUUGCAAAUAUAUAA
...((((((((..(((((((((......)))))))))....(((.(((....))))))....))))))))................(((..((((....))))..))).......... ( -38.60)
>DroYak_CAF1 23285 117 - 1
GGGCUAGCGACAAAAACAGCUGAUCUGACAGCUGCUCGCACGGAUGCCAGACGGUACCAAGAGAUGCCAGAUAAUUUGGAUCAACCGCAU-UUUAAAAUUGAAAUUGCACAUAUUACA
((....((((......((((((......)))))).))))..((.((((....))))))....(((.(((((...))))))))..))((((-((((....))))).))).......... ( -29.10)
>consensus
GGGCUGGCAGCAACAACAGCUGAUCUGACAGCUGUUCGCACGGAUGCCAGAAGGUUACAAGAGCUGCCAGAUUAUUUGGAGCAACCGCAUUUUAAAAUUUGAAAUUGCA_____AAAA
...((((((((....(((((((......))))))).......(..(((....)))..)....))))))))................................................ (-21.46 = -22.34 +   0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,939,403 – 7,939,515
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 90.54
Mean single sequence MFE -35.86
Consensus MFE -28.22
Energy contribution -28.38
Covariance contribution 0.16
Combinations/Pair 1.21
Mean z-score -2.00
Structure conservation index 0.79
SVM decision value 1.09
SVM RNA-class probability 0.913560
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7939403 112 + 20766785
CAAAAUAAUCUGGCAGCUCUUGCAACCUUAUGGCAUCCGUGCGAACAGCUGUCAGAUCAGCUGUUGUUGUUUCCAGCCCUGGUUUGGGAAAAUUUCACGGCCAACAACCGAA
.......(((((((((((.(((((.((....))......)))))..)))))))))))..(((((.....((((((((....).)))))))......)))))........... ( -33.60)
>DroSec_CAF1 17859 112 + 1
CCAAAUAAUCUGGCAGCUCUUGUAACCUUCUGGCAACGGUGCGGACAGCUUUCAGAUCAGCUGUUGUUGCUGCCAGCCCUGGUUAGGGAAAAUUUCACGGCCAACAACCAAA
((.......((((((((........((..(((....)))...))((((((........))))))....))))))))((((....))))..........))............ ( -33.80)
>DroSim_CAF1 19421 112 + 1
CCAAAUAAUCUGGCAGCUCUUGUAACCUUCUGGCAACGGUGCGGACAGCUGUCAGAUCAGCUGUUGUUGCUGCCAGCCCUGGUUAGGGAAAAUUUCACGGCCAACAACCAAA
((.......((((((((........((..(((....)))...))(((((((......)))))))....))))))))((((....))))..........))............ ( -37.50)
>DroEre_CAF1 16308 112 + 1
CCAAAUCAUCUGGCAGCUCUUGGAACCUUCUGGCAUCCGUGUGAACAGCUGUCAGAUCAGCUGUUCUUACUGCCAGCCCUGGUUUGGGAAAAUUUCACGGCCAACAACCGAA
((((((((.(((((((.....(((.((....))..)))....(((((((((......)))))))))...)))))))...))))))))..........(((.......))).. ( -42.80)
>DroYak_CAF1 23323 112 + 1
CCAAAUUAUCUGGCAUCUCUUGGUACCGUCUGGCAUCCGUGCGAGCAGCUGUCAGAUCAGCUGUUUUUGUCGCUAGCCCUGGUUUGGGAAAAUUUCACGGCCAACAACCGAA
((((((((.(((((........((((.(........).))))(((((((((......))))))))).....)))))...))))))))..........(((.......))).. ( -31.60)
>consensus
CCAAAUAAUCUGGCAGCUCUUGGAACCUUCUGGCAUCCGUGCGAACAGCUGUCAGAUCAGCUGUUGUUGCUGCCAGCCCUGGUUUGGGAAAAUUUCACGGCCAACAACCGAA
.........((((((((...............(((....))).((((((((......))))))))...))))))))(((......)))..........((.......))... (-28.22 = -28.38 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,939,403 – 7,939,515
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 90.54
Mean single sequence MFE -38.85
Consensus MFE -28.68
Energy contribution -29.16
Covariance contribution 0.48
Combinations/Pair 1.12
Mean z-score -2.11
Structure conservation index 0.74
SVM decision value 0.60
SVM RNA-class probability 0.795063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7939403 112 - 20766785
UUCGGUUGUUGGCCGUGAAAUUUUCCCAAACCAGGGCUGGAAACAACAACAGCUGAUCUGACAGCUGUUCGCACGGAUGCCAUAAGGUUGCAAGAGCUGCCAGAUUAUUUUG
.(((((((((((((.((..............)).)))((....)).))))))))))((((.(((((.((.(((.....(((....)))))))).))))).))))........ ( -39.84)
>DroSec_CAF1 17859 112 - 1
UUUGGUUGUUGGCCGUGAAAUUUUCCCUAACCAGGGCUGGCAGCAACAACAGCUGAUCUGAAAGCUGUCCGCACCGUUGCCAGAAGGUUACAAGAGCUGCCAGAUUAUUUGG
....(((((..(((.((..............)).)))..))))).....(((.(((((((..(((((....)...((.(((....))).))...))))..))))))).))). ( -35.44)
>DroSim_CAF1 19421 112 - 1
UUUGGUUGUUGGCCGUGAAAUUUUCCCUAACCAGGGCUGGCAGCAACAACAGCUGAUCUGACAGCUGUCCGCACCGUUGCCAGAAGGUUACAAGAGCUGCCAGAUUAUUUGG
....(((((..(((.((..............)).)))..))))).....(((.(((((((.((((((....)...((.(((....))).))...))))).))))))).))). ( -37.94)
>DroEre_CAF1 16308 112 - 1
UUCGGUUGUUGGCCGUGAAAUUUUCCCAAACCAGGGCUGGCAGUAAGAACAGCUGAUCUGACAGCUGUUCACACGGAUGCCAGAAGGUUCCAAGAGCUGCCAGAUGAUUUGG
..((((.....))))..........(((((.((...((((((((..(((((((((......)))))))))....(((.(((....))))))....)))))))).)).))))) ( -45.80)
>DroYak_CAF1 23323 112 - 1
UUCGGUUGUUGGCCGUGAAAUUUUCCCAAACCAGGGCUAGCGACAAAAACAGCUGAUCUGACAGCUGCUCGCACGGAUGCCAGACGGUACCAAGAGAUGCCAGAUAAUUUGG
....((((((((((.((..............)).)))))))))).....((((((......))))))(((....((.((((....))))))..)))...(((((...))))) ( -35.24)
>consensus
UUCGGUUGUUGGCCGUGAAAUUUUCCCAAACCAGGGCUGGCAGCAACAACAGCUGAUCUGACAGCUGUUCGCACGGAUGCCAGAAGGUUACAAGAGCUGCCAGAUUAUUUGG
....((((((((((.((..............)).)))))))))).....(((.(((((((.((((((....)...(..(((....)))..)...))))).))))))).))). (-28.68 = -29.16 +   0.48)

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 10:21:52 2006